diff --git a/.gitignore b/.gitignore
index cb95d1259483cf134e476684b1d08738b02270c7..35641d7028936ac3be8cf96cc0d37b1d85cb2dfa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
nextflow
.nextflow.log*
.nextflow/
diff --git a/.gitmodules b/.gitmodules
index 50c6c3ba42c9e5cd6a12a316cb4766cb4b0c6f61..da4a8214e1c7e0b79f6db0045b2cd16cd1783a32 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
[submodule "src/.docker_modules/hicstuff/3.1.3/hicstuff"]
path = src/.docker_modules/hicstuff/3.1.3/hicstuff
url = git@github.com:koszullab/hicstuff.git
diff --git a/.reuse/dep5 b/.reuse/dep5
new file mode 100644
index 0000000000000000000000000000000000000000..0f096e979b5e9e25d71019f5c6fad4dc826e0d4a
--- /dev/null
+++ b/.reuse/dep5
@@ -0,0 +1,10 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: nextflow
+Upstream-Contact: Laurent Modolo <laurent.modolo@ens-lyon.fr>
+Source: https://gitbio.ens-lyon.fr/LBMC/nextflow
+
+# Sample paragraph, commented out:
+#
+# Files: src/*
+# Copyright: $YEAR $NAME <$CONTACT>
+# License: ...
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 03648b4bcba3a59235e177281406520da2dc4239..f62c57f4fdaa89a898601638b2bcd1e6910c284a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
# Changelog
All notable changes to this project will be documented in this file.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 2b87ac37aa1cb54f4a56c8c3b91a3ffd4f55f15f..16e888fc557cc11e99eaeee72b72459c747690bf 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
# Contributing
When contributing to this repository, please first discuss the change you wish to make via issues,
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index d290c0694a6f52bee4b4d955fa67212bd072fecc..0000000000000000000000000000000000000000
--- a/LICENSE
+++ /dev/null
@@ -1,518 +0,0 @@
-
- CeCILL FREE SOFTWARE LICENSE AGREEMENT
-
-Version 2.1 dated 2013-06-21
-
-
- Notice
-
-This Agreement is a Free Software license agreement that is the result
-of discussions between its authors in order to ensure compliance with
-the two main principles guiding its drafting:
-
- * firstly, compliance with the principles governing the distribution
- of Free Software: access to source code, broad rights granted to users,
- * secondly, the election of a governing law, French law, with which it
- is conformant, both as regards the law of torts and intellectual
- property law, and the protection that it offers to both authors and
- holders of the economic rights over software.
-
-The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
-license are:
-
-Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
-public scientific, technical and industrial research establishment,
-having its principal place of business at 25 rue Leblanc, immeuble Le
-Ponant D, 75015 Paris, France.
-
-Centre National de la Recherche Scientifique - CNRS, a public scientific
-and technological establishment, having its principal place of business
-at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique -
-Inria, a public scientific and technological establishment, having its
-principal place of business at Domaine de Voluceau, Rocquencourt, BP
-105, 78153 Le Chesnay cedex, France.
-
-
- Preamble
-
-The purpose of this Free Software license agreement is to grant users
-the right to modify and redistribute the software governed by this
-license within the framework of an open source distribution model.
-
-The exercising of this right is conditional upon certain obligations for
-users so as to preserve this status for all subsequent redistributions.
-
-In consideration of access to the source code and the rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors only have limited liability.
-
-In this respect, the risks associated with loading, using, modifying
-and/or developing or reproducing the software by the user are brought to
-the user's attention, given its Free Software status, which may make it
-complicated to use, with the result that its use is reserved for
-developers and experienced professionals having in-depth computer
-knowledge. Users are therefore encouraged to load and test the
-suitability of the software as regards their requirements in conditions
-enabling the security of their systems and/or data to be ensured and,
-more generally, to use and operate it in the same conditions of
-security. This Agreement may be freely reproduced and published,
-provided it is not altered, and that no provisions are either added or
-removed herefrom.
-
-This Agreement may apply to any or all software for which the holder of
-the economic rights decides to submit the use thereof to its provisions.
-
-Frequently asked questions can be found on the official website of the
-CeCILL licenses family (http://www.cecill.info/index.en.html) for any
-necessary clarification.
-
-
- Article 1 - DEFINITIONS
-
-For the purpose of this Agreement, when the following expressions
-commence with a capital letter, they shall have the following meaning:
-
-Agreement: means this license agreement, and its possible subsequent
-versions and annexes.
-
-Software: means the software in its Object Code and/or Source Code form
-and, where applicable, its documentation, "as is" when the Licensee
-accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and possibly its
-Object Code form and, where applicable, its documentation, "as is" when
-it is first distributed under the terms and conditions of the Agreement.
-
-Modified Software: means the Software modified by at least one
-Contribution.
-
-Source Code: means all the Software's instructions and program lines to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of
-the Source Code.
-
-Holder: means the holder(s) of the economic rights over the Initial
-Software.
-
-Licensee: means the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any other individual or legal entity, who
-distributes the Software under the Agreement.
-
-Contribution: means any or all modifications, corrections, translations,
-adaptations and/or new functions integrated into the Software by any or
-all Contributors, as well as any or all Internal Modules.
-
-Module: means a set of sources files including their documentation that
-enables supplementary functions or services in addition to those offered
-by the Software.
-
-External Module: means any or all Modules, not derived from the
-Software, so that this Module and the Software run in separate address
-spaces, with one calling the other when they are run.
-
-Internal Module: means any or all Module, connected to the Software so
-that they both execute in the same address space.
-
-GNU GPL: means the GNU General Public License version 2 or any
-subsequent version, as published by the Free Software Foundation Inc.
-
-GNU Affero GPL: means the GNU Affero General Public License version 3 or
-any subsequent version, as published by the Free Software Foundation Inc.
-
-EUPL: means the European Union Public License version 1.1 or any
-subsequent version, as published by the European Commission.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
- Article 2 - PURPOSE
-
-The purpose of the Agreement is the grant by the Licensor to the
-Licensee of a non-exclusive, transferable and worldwide license for the
-Software as set forth in Article 5 <#scope> hereinafter for the whole
-term of the protection granted by the rights over said Software.
-
-
- Article 3 - ACCEPTANCE
-
-3.1 The Licensee shall be deemed as having accepted the terms and
-conditions of this Agreement upon the occurrence of the first of the
-following events:
-
- * (i) loading the Software by any or all means, notably, by
- downloading from a remote server, or by loading from a physical medium;
- * (ii) the first time the Licensee exercises any of the rights granted
- hereunder.
-
-3.2 One copy of the Agreement, containing a notice relating to the
-characteristics of the Software, to the limited warranty, and to the
-fact that its use is restricted to experienced users has been provided
-to the Licensee prior to its acceptance as set forth in Article 3.1
-<#accepting> hereinabove, and the Licensee hereby acknowledges that it
-has read and understood it.
-
-
- Article 4 - EFFECTIVE DATE AND TERM
-
-
- 4.1 EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by
-the Licensee as set forth in Article 3.1 <#accepting>.
-
-
- 4.2 TERM
-
-The Agreement shall remain in force for the entire legal term of
-protection of the economic rights over the Software.
-
-
- Article 5 - SCOPE OF RIGHTS GRANTED
-
-The Licensor hereby grants to the Licensee, who accepts, the following
-rights over the Software for any or all use, and for the term of the
-Agreement, on the basis of the terms and conditions set forth hereinafter.
-
-Besides, if the Licensor owns or comes to own one or more patents
-protecting all or part of the functions of the Software or of its
-components, the Licensor undertakes not to enforce the rights granted by
-these patents against successive Licensees using, exploiting or
-modifying the Software. If these patents are transferred, the Licensor
-undertakes to have the transferees subscribe to the obligations set
-forth in this paragraph.
-
-
- 5.1 RIGHT OF USE
-
-The Licensee is authorized to use the Software, without any limitation
-as to its fields of application, with it being hereinafter specified
-that this comprises:
-
- 1. permanent or temporary reproduction of all or part of the Software
- by any or all means and in any or all form.
-
- 2. loading, displaying, running, or storing the Software on any or all
- medium.
-
- 3. entitlement to observe, study or test its operation so as to
- determine the ideas and principles behind any or all constituent
- elements of said Software. This shall apply when the Licensee
- carries out any or all loading, displaying, running, transmission or
- storage operation as regards the Software, that it is entitled to
- carry out hereunder.
-
-
- 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
-
-The right to make Contributions includes the right to translate, adapt,
-arrange, or make any or all modifications to the Software, and the right
-to reproduce the resulting software.
-
-The Licensee is authorized to make any or all Contributions to the
-Software provided that it includes an explicit notice that it is the
-author of said Contribution and indicates the date of the creation thereof.
-
-
- 5.3 RIGHT OF DISTRIBUTION
-
-In particular, the right of distribution includes the right to publish,
-transmit and communicate the Software to the general public on any or
-all medium, and by any or all means, and the right to market, either in
-consideration of a fee, or free of charge, one or more copies of the
-Software by any means.
-
-The Licensee is further authorized to distribute copies of the modified
-or unmodified Software to third parties according to the terms and
-conditions set forth hereinafter.
-
-
- 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to distribute true copies of the Software in
-Source Code or Object Code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
- 1. a copy of the Agreement,
-
- 2. a notice relating to the limitation of both the Licensor's warranty
- and liability as set forth in Articles 8 and 9,
-
-and that, in the event that only the Object Code of the Software is
-redistributed, the Licensee allows effective access to the full Source
-Code of the Software for a period of at least three years from the
-distribution of the Software, it being understood that the additional
-acquisition cost of the Source Code shall not exceed the cost of the
-data transfer.
-
-
- 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
-
-When the Licensee makes a Contribution to the Software, the terms and
-conditions for the distribution of the resulting Modified Software
-become subject to all the provisions of this Agreement.
-
-The Licensee is authorized to distribute the Modified Software, in
-source code or object code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
- 1. a copy of the Agreement,
-
- 2. a notice relating to the limitation of both the Licensor's warranty
- and liability as set forth in Articles 8 and 9,
-
-and, in the event that only the object code of the Modified Software is
-redistributed,
-
- 3. a note stating the conditions of effective access to the full source
- code of the Modified Software for a period of at least three years
- from the distribution of the Modified Software, it being understood
- that the additional acquisition cost of the source code shall not
- exceed the cost of the data transfer.
-
-
- 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
-
-When the Licensee has developed an External Module, the terms and
-conditions of this Agreement do not apply to said External Module, that
-may be distributed under a separate license agreement.
-
-
- 5.3.4 COMPATIBILITY WITH OTHER LICENSES
-
-The Licensee can include a code that is subject to the provisions of one
-of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
-Modified or unmodified Software, and distribute that entire code under
-the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
-
-The Licensee can include the Modified or unmodified Software in a code
-that is subject to the provisions of one of the versions of the GNU GPL,
-GNU Affero GPL and/or EUPL and distribute that entire code under the
-terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
-
-
- Article 6 - INTELLECTUAL PROPERTY
-
-
- 6.1 OVER THE INITIAL SOFTWARE
-
-The Holder owns the economic rights over the Initial Software. Any or
-all use of the Initial Software is subject to compliance with the terms
-and conditions under which the Holder has elected to distribute its work
-and no one shall be entitled to modify the terms and conditions for the
-distribution of said Initial Software.
-
-The Holder undertakes that the Initial Software will remain ruled at
-least by this Agreement, for the duration set forth in Article 4.2 <#term>.
-
-
- 6.2 OVER THE CONTRIBUTIONS
-
-The Licensee who develops a Contribution is the owner of the
-intellectual property rights over this Contribution as defined by
-applicable law.
-
-
- 6.3 OVER THE EXTERNAL MODULES
-
-The Licensee who develops an External Module is the owner of the
-intellectual property rights over this External Module as defined by
-applicable law and is free to choose the type of agreement that shall
-govern its distribution.
-
-
- 6.4 JOINT PROVISIONS
-
-The Licensee expressly undertakes:
-
- 1. not to remove, or modify, in any manner, the intellectual property
- notices attached to the Software;
-
- 2. to reproduce said notices, in an identical manner, in the copies of
- the Software modified or not.
-
-The Licensee undertakes not to directly or indirectly infringe the
-intellectual property rights on the Software of the Holder and/or
-Contributors, and to take, where applicable, vis-Ã -vis its staff, any
-and all measures required to ensure respect of said intellectual
-property rights of the Holder and/or Contributors.
-
-
- Article 7 - RELATED SERVICES
-
-7.1 Under no circumstances shall the Agreement oblige the Licensor to
-provide technical assistance or maintenance services for the Software.
-
-However, the Licensor is entitled to offer this type of services. The
-terms and conditions of such technical assistance, and/or such
-maintenance, shall be set forth in a separate instrument. Only the
-Licensor offering said maintenance and/or technical assistance services
-shall incur liability therefor.
-
-7.2 Similarly, any Licensor is entitled to offer to its licensees, under
-its sole responsibility, a warranty, that shall only be binding upon
-itself, for the redistribution of the Software and/or the Modified
-Software, under terms and conditions that it is free to decide. Said
-warranty, and the financial terms and conditions of its application,
-shall be subject of a separate instrument executed between the Licensor
-and the Licensee.
-
-
- Article 8 - LIABILITY
-
-8.1 Subject to the provisions of Article 8.2, the Licensee shall be
-entitled to claim compensation for any direct loss it may have suffered
-from the Software as a result of a fault on the part of the relevant
-Licensor, subject to providing evidence thereof.
-
-8.2 The Licensor's liability is limited to the commitments made under
-this Agreement and shall not be incurred as a result of in particular:
-(i) loss due the Licensee's total or partial failure to fulfill its
-obligations, (ii) direct or consequential loss that is suffered by the
-Licensee due to the use or performance of the Software, and (iii) more
-generally, any consequential loss. In particular the Parties expressly
-agree that any or all pecuniary or business loss (i.e. loss of data,
-loss of profits, operating loss, loss of customers or orders,
-opportunity cost, any disturbance to business activities) or any or all
-legal proceedings instituted against the Licensee by a third party,
-shall constitute consequential loss and shall not provide entitlement to
-any or all compensation from the Licensor.
-
-
- Article 9 - WARRANTY
-
-9.1 The Licensee acknowledges that the scientific and technical
-state-of-the-art when the Software was distributed did not enable all
-possible uses to be tested and verified, nor for the presence of
-possible defects to be detected. In this respect, the Licensee's
-attention has been drawn to the risks associated with loading, using,
-modifying and/or developing and reproducing the Software which are
-reserved for experienced users.
-
-The Licensee shall be responsible for verifying, by any or all means,
-the suitability of the product for its requirements, its good working
-order, and for ensuring that it shall not cause damage to either persons
-or properties.
-
-9.2 The Licensor hereby represents, in good faith, that it is entitled
-to grant all the rights over the Software (including in particular the
-rights set forth in Article 5 <#scope>).
-
-9.3 The Licensee acknowledges that the Software is supplied "as is" by
-the Licensor without any other express or tacit warranty, other than
-that provided for in Article 9.2 <#good-faith> and, in particular,
-without any warranty as to its commercial value, its secured, safe,
-innovative or relevant nature.
-
-Specifically, the Licensor does not warrant that the Software is free
-from any error, that it will operate without interruption, that it will
-be compatible with the Licensee's own equipment and software
-configuration, nor that it will meet the Licensee's requirements.
-
-9.4 The Licensor does not either expressly or tacitly warrant that the
-Software does not infringe any third party intellectual property right
-relating to a patent, software or any other property right. Therefore,
-the Licensor disclaims any and all liability towards the Licensee
-arising out of any or all proceedings for infringement that may be
-instituted in respect of the use, modification and redistribution of the
-Software. Nevertheless, should such proceedings be instituted against
-the Licensee, the Licensor shall provide it with technical and legal
-expertise for its defense. Such technical and legal expertise shall be
-decided on a case-by-case basis between the relevant Licensor and the
-Licensee pursuant to a memorandum of understanding. The Licensor
-disclaims any and all liability as regards the Licensee's use of the
-name of the Software. No warranty is given as regards the existence of
-prior rights over the name of the Software or as regards the existence
-of a trademark.
-
-
- Article 10 - TERMINATION
-
-10.1 In the event of a breach by the Licensee of its obligations
-hereunder, the Licensor may automatically terminate this Agreement
-thirty (30) days after notice has been sent to the Licensee and has
-remained ineffective.
-
-10.2 A Licensee whose Agreement is terminated shall no longer be
-authorized to use, modify or distribute the Software. However, any
-licenses that it may have granted prior to termination of the Agreement
-shall remain valid subject to their having been granted in compliance
-with the terms and conditions hereof.
-
-
- Article 11 - MISCELLANEOUS
-
-
- 11.1 EXCUSABLE EVENTS
-
-Neither Party shall be liable for any or all delay, or failure to
-perform the Agreement, that may be attributable to an event of force
-majeure, an act of God or an outside cause, such as defective
-functioning or interruptions of the electricity or telecommunications
-networks, network paralysis following a virus attack, intervention by
-government authorities, natural disasters, water damage, earthquakes,
-fire, explosions, strikes and labor unrest, war, etc.
-
-11.2 Any failure by either Party, on one or more occasions, to invoke
-one or more of the provisions hereof, shall under no circumstances be
-interpreted as being a waiver by the interested Party of its right to
-invoke said provision(s) subsequently.
-
-11.3 The Agreement cancels and replaces any or all previous agreements,
-whether written or oral, between the Parties and having the same
-purpose, and constitutes the entirety of the agreement between said
-Parties concerning said purpose. No supplement or modification to the
-terms and conditions hereof shall be effective as between the Parties
-unless it is made in writing and signed by their duly authorized
-representatives.
-
-11.4 In the event that one or more of the provisions hereof were to
-conflict with a current or future applicable act or legislative text,
-said act or legislative text shall prevail, and the Parties shall make
-the necessary amendments so as to comply with said act or legislative
-text. All other provisions shall remain effective. Similarly, invalidity
-of a provision of the Agreement, for any reason whatsoever, shall not
-cause the Agreement as a whole to be invalid.
-
-
- 11.5 LANGUAGE
-
-The Agreement is drafted in both French and English and both versions
-are deemed authentic.
-
-
- Article 12 - NEW VERSIONS OF THE AGREEMENT
-
-12.1 Any person is authorized to duplicate and distribute copies of this
-Agreement.
-
-12.2 So as to ensure coherence, the wording of this Agreement is
-protected and may only be modified by the authors of the License, who
-reserve the right to periodically publish updates or new versions of the
-Agreement, each with a separate number. These subsequent versions may
-address new issues encountered by Free Software.
-
-12.3 Any Software distributed under a given version of the Agreement may
-only be subsequently distributed under the same version of the Agreement
-or a subsequent version, subject to the provisions of Article 5.3.4
-<#compatibility>.
-
-
- Article 13 - GOVERNING LAW AND JURISDICTION
-
-13.1 The Agreement is governed by French law. The Parties agree to
-endeavor to seek an amicable solution to any disagreements or disputes
-that may arise during the performance of the Agreement.
-
-13.2 Failing an amicable solution within two (2) months as from their
-occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the more diligent Party.
diff --git a/LICENSES/AGPL-3.0-or-later.txt b/LICENSES/AGPL-3.0-or-later.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c97efd25b5974b974ed9a8a18207bc4f55bb338
--- /dev/null
+++ b/LICENSES/AGPL-3.0-or-later.txt
@@ -0,0 +1,235 @@
+GNU AFFERO GENERAL PUBLIC LICENSE
+Version 3, 19 November 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
+
+ Preamble
+
+The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software.
+
+The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, our General Public Licenses are intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users.
+
+When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.
+
+Developers that use our General Public Licenses protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License which gives you legal permission to copy, distribute and/or modify the software.
+
+A secondary benefit of defending all users' freedom is that improvements made in alternate versions of the program, if they receive widespread use, become available for other developers to incorporate. Many developers of free software are heartened and encouraged by the resulting cooperation. However, in the case of software used on network servers, this result may fail to come about. The GNU General Public License permits making a modified version and letting the public access it on a server without ever releasing its source code to the public.
+
+The GNU Affero General Public License is designed specifically to ensure that, in such cases, the modified source code becomes available to the community. It requires the operator of a network server to provide the source code of the modified version running there to the users of that server. Therefore, public use of a modified version, on a publicly accessible server, gives the public access to the source code of the modified version.
+
+An older license, called the Affero General Public License and published by Affero, was designed to accomplish similar goals. This is a different license, not a version of the Affero GPL, but Affero has released a new version of the Affero GPL which permits relicensing under this license.
+
+The precise terms and conditions for copying, distribution and modification follow.
+
+ TERMS AND CONDITIONS
+
+0. Definitions.
+
+"This License" refers to version 3 of the GNU Affero General Public License.
+
+"Copyright" also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.
+
+"The Program" refers to any copyrightable work licensed under this License. Each licensee is addressed as "you". "Licensees" and "recipients" may be individuals or organizations.
+
+To "modify" a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a "modified version" of the earlier work or a work "based on" the earlier work.
+
+A "covered work" means either the unmodified Program or a work based on the Program.
+
+To "propagate" a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well.
+
+To "convey" a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.
+
+An interactive user interface displays "Appropriate Legal Notices" to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.
+
+1. Source Code.
+The "source code" for a work means the preferred form of the work for making modifications to it. "Object code" means any non-source form of a work.
+
+A "Standard Interface" means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.
+
+The "System Libraries" of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A "Major Component", in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.
+
+The "Corresponding Source" for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.
+
+The Corresponding Source for a work in source code form is that same work.
+
+2. Basic Permissions.
+All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.
+
+You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.
+
+Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.
+
+3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.
+
+When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures.
+
+4. Conveying Verbatim Copies.
+You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.
+
+You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.
+
+5. Conveying Modified Source Versions.
+You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:
+
+ a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
+
+ b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. This requirement modifies the requirement in section 4 to "keep intact all notices".
+
+ c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it.
+
+ d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so.
+
+A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an "aggregate" if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.
+
+6. Conveying Non-Source Forms.
+You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:
+
+ a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
+
+ b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge.
+
+ c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b.
+
+ d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements.
+
+ e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d.
+
+A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work.
+
+A "User Product" is either (1) a "consumer product", which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, "normally used" refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product.
+
+"Installation Information" for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.
+
+If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).
+
+The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.
+
+Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.
+
+7. Additional Terms.
+"Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.
+
+When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.
+
+Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:
+
+ a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
+
+ b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
+
+ c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or
+
+ d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
+
+ e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
+
+ f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors.
+
+All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.
+
+If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.
+
+Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.
+
+8. Termination.
+
+You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).
+
+However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
+
+Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.
+
+Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.
+
+9. Acceptance Not Required for Having Copies.
+
+You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.
+
+10. Automatic Licensing of Downstream Recipients.
+
+Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.
+
+An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.
+
+You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.
+
+11. Patents.
+
+A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's "contributor version".
+
+A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.
+
+Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.
+
+In the following three paragraphs, a "patent license" is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.
+
+If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.
+
+A patent license is "discriminatory" if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.
+
+12. No Surrender of Others' Freedom.
+
+If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.
+
+13. Remote Network Interaction; Use with the GNU General Public License.
+
+Notwithstanding any other provision of this License, if you modify the Program, your modified version must prominently offer all users interacting with it remotely through a computer network (if your version supports such interaction) an opportunity to receive the Corresponding Source of your version by providing access to the Corresponding Source from a network server at no charge, through some standard or customary means of facilitating copying of software. This Corresponding Source shall include the Corresponding Source for any work covered by version 3 of the GNU General Public License that is incorporated pursuant to the following paragraph.
+
+Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the work with which it is combined will remain governed by version 3 of the GNU General Public License.
+
+14. Revised Versions of this License.
+
+The Free Software Foundation may publish revised and/or new versions of the GNU Affero General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU Affero General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU Affero General Public License, you may choose any version ever published by the Free Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU Affero General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.
+
+15. Disclaimer of Warranty.
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+16. Limitation of Liability.
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+17. Interpretation of Sections 15 and 16.
+
+If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.
+
+END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If your software can interact with users remotely through a computer network, you should also make sure that it provides a way for users to get its source. For example, if your program is a web application, its interface could display a "Source" link that leads users to an archive of the code. There are many ways you could offer source, and different solutions will be better for different programs; see section 13 for the specific requirements.
+
+You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU AGPL, see <http://www.gnu.org/licenses/>.
diff --git a/LICENSES/CC-BY-SA-4.0.txt b/LICENSES/CC-BY-SA-4.0.txt
new file mode 100644
index 0000000000000000000000000000000000000000..835a6836b385fa068fdd625685548845cda60c2f
--- /dev/null
+++ b/LICENSES/CC-BY-SA-4.0.txt
@@ -0,0 +1,170 @@
+Creative Commons Attribution-ShareAlike 4.0 International
+
+ Creative Commons Corporation (“Creative Commonsâ€) is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an “as-is†basis. Creative Commons gives no warranties regarding its licenses, any material licensed under their terms and conditions, or any related information. Creative Commons disclaims all liability for damages resulting from their use to the fullest extent possible.
+
+Using Creative Commons Public Licenses
+
+Creative Commons public licenses provide a standard set of terms and conditions that creators and other rights holders may use to share original works of authorship and other material subject to copyright and certain other rights specified in the public license below. The following considerations are for informational purposes only, are not exhaustive, and do not form part of our licenses.
+
+Considerations for licensors: Our public licenses are intended for use by those authorized to give the public permission to use material in ways otherwise restricted by copyright and certain other rights. Our licenses are irrevocable. Licensors should read and understand the terms and conditions of the license they choose before applying it. Licensors should also secure all rights necessary before applying our licenses so that the public can reuse the material as expected. Licensors should clearly mark any material not subject to the license. This includes other CC-licensed material, or material used under an exception or limitation to copyright. More considerations for licensors.
+
+Considerations for the public: By using one of our public licenses, a licensor grants the public permission to use the licensed material under specified terms and conditions. If the licensor’s permission is not necessary for any reason–for example, because of any applicable exception or limitation to copyright–then that use is not regulated by the license. Our licenses grant only permissions under copyright and certain other rights that a licensor has authority to grant. Use of the licensed material may still be restricted for other reasons, including because others have copyright or other rights in the material. A licensor may make special requests, such as asking that all changes be marked or described.
+
+Although not required by our licenses, you are encouraged to respect those requests where reasonable. More considerations for the public.
+
+Creative Commons Attribution-ShareAlike 4.0 International Public License
+
+By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-ShareAlike 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
+
+Section 1 – Definitions.
+
+ a. Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.
+
+ b. Adapter's License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License.
+
+ c. BY-SA Compatible License means a license listed at creativecommons.org/compatiblelicenses, approved by Creative Commons as essentially the equivalent of this Public License.
+
+ d. Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.
+
+ e. Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.
+
+ f. Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
+
+ g. License Elements means the license attributes listed in the name of a Creative Commons Public License. The License Elements of this Public License are Attribution and ShareAlike.
+
+ h. Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License.
+
+ i. Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.
+
+ j. Licensor means the individual(s) or entity(ies) granting rights under this Public License.
+
+ k. Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.
+
+ l. Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.
+
+ m. You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.
+
+Section 2 – Scope.
+
+ a. License grant.
+
+ 1. Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:
+
+ A. reproduce and Share the Licensed Material, in whole or in part; and
+
+ B. produce, reproduce, and Share Adapted Material.
+
+ 2. Exceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions.
+
+ 3. Term. The term of this Public License is specified in Section 6(a).
+
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+ 6. No endorsement. Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i).
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+ 1. Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.
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+ 3. To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties.
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+Your exercise of the Licensed Rights is expressly made subject to the following conditions.
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+
+ 3. If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable.
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+ b. ShareAlike.In addition to the conditions in Section 3(a), if You Share Adapted Material You produce, the following conditions also apply.
+
+ 1. The Adapter’s License You apply must be a Creative Commons license with the same License Elements, this version or later, or a BY-SA Compatible License.
+
+ 2. You must include the text of, or the URI or hyperlink to, the Adapter's License You apply. You may satisfy this condition in any reasonable manner based on the medium, means, and context in which You Share Adapted Material.
+
+ 3. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, Adapted Material that restrict exercise of the rights granted under the Adapter's License You apply.
+
+Section 4 – Sui Generis Database Rights.
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+ c. You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database.
+For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.
+
+Section 5 – Disclaimer of Warranties and Limitation of Liability.
+
+ a. Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.
+
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+
+ c. The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability.
+
+Section 6 – Term and Termination.
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+ a. This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically.
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+ b. Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates:
+
+ 1. automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or
+
+ 2. upon express reinstatement by the Licensor.
+
+ c. For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License.
+
+ d. For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License.
+
+ e. Sections 1, 5, 6, 7, and 8 survive termination of this Public License.
+
+Section 7 – Other Terms and Conditions.
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+ a. The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.
+
+ b. Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License.
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+Section 8 – Interpretation.
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+ a. For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.
+
+ b. To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.
+
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+
+Creative Commons is not a party to its public licenses. Notwithstanding, Creative Commons may elect to apply one of its public licenses to material it publishes and in those instances will be considered the “Licensor.†Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at creativecommons.org/policies, Creative Commons does not authorize the use of the trademark “Creative Commons†or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses.
+
+Creative Commons may be contacted at creativecommons.org.
diff --git a/README.md b/README.md
index cab03de46f2c5c7a9408511c29ad98385b3c8394..9685f60044b0a68230ae5b3ac98e578aa6e7491f 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
# nextflow pipeline
This repository is a template and a library repository to help you build nextflow pipeline.
diff --git a/bin/.gitignore b/bin/.gitignore
index 72e8ffc0db8aad71a934dd11e5968bd5109e54b4..8a8feafc11a33ce80e2a8572af3ad268ee8b73eb 100644
--- a/bin/.gitignore
+++ b/bin/.gitignore
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
*
diff --git a/data/.gitignore b/data/.gitignore
index 72e8ffc0db8aad71a934dd11e5968bd5109e54b4..8a8feafc11a33ce80e2a8572af3ad268ee8b73eb 100644
--- a/data/.gitignore
+++ b/data/.gitignore
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
*
diff --git a/doc/.gitignore b/doc/.gitignore
index a1363379944a5745ceb49c0e493d80eb9335c79a..7499200f5fc7d5c90da0ec32b2b6ace5dc5948ef 100644
--- a/doc/.gitignore
+++ b/doc/.gitignore
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
*.pdf
diff --git a/doc/building_your_pipeline.md b/doc/building_your_pipeline.md
index 90fba56d210c3bc229a6beb173e608214ddcc30c..4db956bbbd33433d481b924038d73028b0a6072e 100644
--- a/doc/building_your_pipeline.md
+++ b/doc/building_your_pipeline.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
# Building your own pipeline
The goal of this guide is to walk you through the Nextflow pipeline building process you will learn:
diff --git a/doc/getting_started.md b/doc/getting_started.md
index e41ffe528fd9745322fec917e00ae407f1a5f389..8a601a98566a4285e5eb574a6d9667a64b201a92 100644
--- a/doc/getting_started.md
+++ b/doc/getting_started.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
# Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
diff --git a/doc/img/fork.png.license b/doc/img/fork.png.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/doc/img/fork.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/doc/img/merge_request.png.license b/doc/img/merge_request.png.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/doc/img/merge_request.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/doc/img/webide.png.license b/doc/img/webide.png.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/doc/img/webide.png.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/doc/mail.txt.license b/doc/mail.txt.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/doc/mail.txt.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/doc/nf_projects.md b/doc/nf_projects.md
index 140a58183532cb245d5869dabefa3bee33702833..03643ed36fa77281b7d6cad290cf4cba3278a2a8 100644
--- a/doc/nf_projects.md
+++ b/doc/nf_projects.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
## Projects using nextflow
This page list existing Nextflow based pipeline projects into different categories
diff --git a/public/TP_computational_biologists.html b/public/TP_computational_biologists.html
deleted file mode 100644
index d34ba8ddae9a9dc51181715f648b9e05109554cd..0000000000000000000000000000000000000000
--- a/public/TP_computational_biologists.html
+++ /dev/null
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-<!DOCTYPE html>
-<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
-<head>
- <meta charset="utf-8" />
- <meta name="generator" content="pandoc" />
- <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
- <title>TP_experimental_biologists</title>
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- </style>
- <!--[if lt IE 9]>
- <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
- <![endif]-->
-</head>
-<body>
-<p>The Goal of this practical is to learn how to build your own pipeline with nextflow and using the tools already <em>wrapped</em>. For this we are going to build a small RNASeq analysis pipeline that should run the following steps:</p>
-<ul>
-<li>remove Illumina adaptors</li>
-<li>trim reads by quality</li>
-<li>build the index of a reference genome</li>
-<li>estimate the amount of RNA fragments mapping to the transcripts of this genome</li>
-</ul>
-<h1 id="initialize-your-own-project">Initialize your own project</h1>
-<p>You are going to build a pipeline for you or your team. So the first step is to create your own project.</p>
-<h2 id="forking">Forking</h2>
-<p>Instead of reinventing the wheel, you can use the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a> as a template. To easily do so, go to the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a> repository and click on the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/forks/new"><strong>fork</strong></a> button.</p>
-<figure>
-<img src="img/fork.png" alt="fork button" /><figcaption>fork button</figcaption>
-</figure>
-<p>In git, the <a href="https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project">action of forking</a> means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository (here <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a>) create a merge request. Merge requests are sent to the source repository to ask the maintainers to integrate modifications.</p>
-<figure>
-<img src="img/merge_request.png" alt="merge request button" /><figcaption>merge request button</figcaption>
-</figure>
-<h2 id="project-organisation">Project organisation</h2>
-<p>This project (and yours) follows the <a href="http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/ressources/good_practice_LBMC">guide of good practices for the LBMC</a></p>
-<p>You are now on the main page of your fork of the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a>. You can explore this project, all the code in it is under the CeCILL licence (in the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/LICENSE">LICENCE</a> file).</p>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md">README.md</a> file contains instructions to run your pipeline and test its installation.</p>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/CONTRIBUTING.md">CONTRIBUTING.md</a> file contains guidelines if you want to contribute to the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a> (making a merge request for example).</p>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/data">data</a> folder will be the place where you store the raw data for your analysis. The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/results">results</a> folder will be the place where you store the results of your analysis.</p>
-<blockquote>
-<p><strong>The content of <code>data</code> and <code>results</code> folders should never be saved on git.</strong></p>
-</blockquote>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/doc">doc</a> folder contains the documentation of this practical course.</p>
-<p>And most interestingly for you, the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src">src</a> contains code to wrap tools. This folder contains two subdirectories. A <code>docker_modules</code>, a <code>nf_modules</code> and a <code>psmn_modules</code> folder.</p>
-<h3 id="docker_modules"><code>docker_modules</code></h3>
-<p>The <code>src/docker_modules</code> contains the code to wrap tools in <a href="https://www.docker.com/what-docker">Docker</a>. <a href="https://www.docker.com/what-docker">Docker</a> is a framework that allows you to execute software within <a href="https://www.docker.com/what-container">containers</a>. The <code>docker_modules</code> contains directory corresponding to tools and subdirectories corresponding to their version.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" title="1"><span class="fu">ls</span> -l src/docker_modules/</a>
-<a class="sourceLine" id="cb1-2" title="2"><span class="ex">rwxr-xr-x</span> 3 laurent _lpoperator 96 May 25 15:42 bedtools/</a>
-<a class="sourceLine" id="cb1-3" title="3"><span class="ex">drwxr-xr-x</span> 4 laurent _lpoperator 128 Jun 5 16:14 bowtie2/</a>
-<a class="sourceLine" id="cb1-4" title="4"><span class="ex">drwxr-xr-x</span> 3 laurent _lpoperator 96 May 25 15:42 fastqc/</a>
-<a class="sourceLine" id="cb1-5" title="5"><span class="ex">drwxr-xr-x</span> 4 laurent _lpoperator 128 Jun 5 16:14 htseq/</a></code></pre></div>
-<p>To each <code>tools/version</code> corresponds two files:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb2-1" title="1"><span class="fu">ls</span> -l src/docker_modules/bowtie2/2.3.4.1/</a>
-<a class="sourceLine" id="cb2-2" title="2"><span class="ex">-rw-r--r--</span> 1 laurent _lpoperator 283 Jun 5 15:07 Dockerfile</a>
-<a class="sourceLine" id="cb2-3" title="3"><span class="ex">-rwxr-xr-x</span> 1 laurent _lpoperator 79 Jun 5 16:18 docker_init.sh*</a></code></pre></div>
-<p>The <code>Dockerfile</code> is the <a href="https://www.docker.com/what-docker">Docker</a> recipe to create a <a href="https://www.docker.com/what-container">container</a> containing <code>Bowtie2</code> in its <code>2.3.4.1</code> version. And the <code>docker_init.sh</code> file is a small script to create the <a href="https://www.docker.com/what-container">container</a> from this recipe.</p>
-<p>By running this script you will be able to easily install tools in different versions on your personal computer and use it in your pipeline. Some of the advantages are:</p>
-<ul>
-<li>Whatever the computer, the installation and the results will be the same</li>
-<li>You can keep <a href="https://www.docker.com/what-container">container</a> for old version of tools and run it on new systems (science = reproducibility)</li>
-<li>You don’t have to bother with tedious installation procedures, somebody else already did the job and wrote a <code>Dockerfile</code>.</li>
-<li>You can easily keep <a href="https://www.docker.com/what-container">containers</a> for different version of the same tools.</li>
-</ul>
-<h3 id="psmn_modules"><code>psmn_modules</code></h3>
-<p>The <code>src/psmn_modules</code> folder is not really there. It’s a submodule of the project <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a>. To populate it locally you can use the following command:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb3-1" title="1"><span class="fu">git</span> submodule init</a></code></pre></div>
-<p>Like the <code>src/docker_modules</code> the <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a> project describe recipes to install tools and use them. The main difference is that you cannot use <a href="https://www.docker.com/what-docker">Docker</a> on the PSMN. Instead you have to use another framework <a href="http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules">Environment Module</a> which allows you to load modules for specific tools and version. The <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/README.md">README.md</a> file of the <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a> repository contains all the instruction to be able to load the modules maintained by the LBMC and present in the <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a> repository.</p>
-<h3 id="nf_modules"><code>nf_modules</code></h3>
-<p>The <code>src/nf_modules</code> folder contains templates of <a href="https://www.nextflow.io/">nextflow</a> wrappers for the tools available in <a href="https://www.docker.com/what-docker">Docker</a> and <a href="http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:psmn">psmn</a>. The details of the <a href="https://www.nextflow.io/">nextflow</a> wrapper will be presented in the next section. Alongside the <code>.nf</code> and <code>.config</code> files, there is a <code>tests.sh</code> script to run test on the tool.</p>
-<h1 id="nextflow-pipeline">Nextflow pipeline</h1>
-<p>A pipeline is a succession of <strong>process</strong>. Each process has data input(s) and optional data output(s). Data flows are modeled as <strong>channels</strong>.</p>
-<h2 id="processes">Processes</h2>
-<p>Here is an example of <strong>process</strong>:</p>
-<pre class="groovy"><code>process sample_fasta {
- input:
-file fasta from fasta_file
-
- output:
-file "sample.fasta" into fasta_sample
-
- script:
-"""
-head ${fasta} > sample.fasta
-"""
-}</code></pre>
-<p>We have the process <code>sample_fasta</code> that takes a <code>fasta_file</code> <strong>channel</strong> as input and as output a <code>fasta_sample</code> <strong>channel</strong>. The process itself is defined in the <code>script:</code> block and within <code>"""</code>.</p>
-<pre class="groovy"><code>input:
-file fasta from fasta_file</code></pre>
-<p>When we zoom on the <code>input:</code> block we see that we define a variable <code>fasta</code> of type <code>file</code> from the <code>fasta_file</code> <strong>channel</strong>. This mean that groovy is going to write a file named as the content of the variable <code>fasta</code> in the root of the folder where <code>script:</code> is executed.</p>
-<pre class="groovy"><code>output:
-file "sample.fasta" into fasta_sample</code></pre>
-<p>At the end of the script, a file named <code>sample.fasta</code> is found in the root the folder where <code>script:</code> is executed and send into the <strong>channel</strong> <code>fasta_sample</code>.</p>
-<p>Using the WebIDE of Gitlab, create a file <code>src/fasta_sampler.nf</code> with this process and commit it to your repository.</p>
-<figure>
-<img src="img/webide.png" alt="webide" /><figcaption>webide</figcaption>
-</figure>
-<h2 id="channels">Channels</h2>
-<p>Why bother with channels? In the above example, the advantages of channels are not really clear. We could have just given the <code>fasta</code> file to the process. But what if we have many fasta files to process? What if we have sub processes to run on each of the sampled fasta files? Nextflow can easily deal with these problems with the help of channels.</p>
-<blockquote>
-<p><strong>Channels</strong> are streams of items that are emitted by a source and consumed by a process. A process with a channel as input will be run on every item send through the channel.</p>
-</blockquote>
-<pre class="groovy"><code>Channel
- .fromPath( "data/tiny_dataset/fasta/*.fasta" )
- .set { fasta_file }</code></pre>
-<p>Here we defined the channel <code>fasta_file</code> that is going to send every fasta file from the folder <code>data/tiny_dataset/fasta/</code> into the process that take it as input.</p>
-<p>Add the definition of the channel to the <code>src/fasta_sampler.nf</code> file and commit it to your repository.</p>
-<h2 id="run-your-pipeline-locally">Run your pipeline locally</h2>
-<p>After writing this first pipeline, you may want to test it. To do that, first clone your repository. To easily do that set the visibility level to <em>public</em> in the settings/General/Permissions page of your project.</p>
-<p>You can then run the following commands to download your project on your computer:</p>
-<p>If you are on a PSMN computer:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb8-1" title="1"><span class="ex">pip</span> install cutadapt=1.14</a>
-<a class="sourceLine" id="cb8-2" title="2"><span class="va">PATH=</span><span class="st">"/scratch/lmodolo/:</span><span class="va">$PATH</span><span class="st">"</span></a>
-<a class="sourceLine" id="cb8-3" title="3"><span class="fu">git</span> config --global http.sslVerify false</a></code></pre></div>
-<p>and then :</p>
-<blockquote>
-<p>Don’t forget to replace <em>https://gitlab.biologie.ens-lyon.fr/</em> by <em>gitlab_lbmc</em> if you are using your own computer</p>
-</blockquote>
-<div class="sourceCode" id="cb9"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb9-1" title="1"><span class="fu">git</span> clone https://gitlab.biologie.ens-lyon.fr/<span class="op"><</span>usr_name<span class="op">></span>/nextflow.git</a>
-<a class="sourceLine" id="cb9-2" title="2"><span class="bu">cd</span> nextflow</a>
-<a class="sourceLine" id="cb9-3" title="3"><span class="ex">src/install_nextflow.sh</span></a></code></pre></div>
-<p>We also need data to run our pipeline:</p>
-<pre><code>cd data
-git clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
-cd ..</code></pre>
-<p>We can run our pipeline with the following command:</p>
-<div class="sourceCode" id="cb11"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb11-1" title="1"><span class="ex">./nextflow</span> src/fasta_sampler.nf</a></code></pre></div>
-<h2 id="getting-your-results">Getting your results</h2>
-<p>Our pipeline seems to work but we don’t know where is the <code>sample.fasta</code>. To get results out of a process, we need to tell nextflow to write it somewhere (we may don’t need to get every intermediate file in our results).</p>
-<p>To do that we need to add the following line before the <code>input:</code> section:</p>
-<pre class="groovy"><code>publishDir "results/sampling/", mode: 'copy'</code></pre>
-<p>Every file described in the <code>output:</code> section will be copied from nextflow to the folder <code>results/sampling/</code>.</p>
-<p>Add this to your <code>src/fasta_sampler.nf</code> file with the WebIDE and commit to your repository. Pull your modifications locally with the command:</p>
-<div class="sourceCode" id="cb13"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb13-1" title="1"><span class="fu">git</span> pull origin master</a></code></pre></div>
-<p>You can run your pipeline again and check the content of the folder <code>results/sampling</code>.</p>
-<h2 id="fasta-everywhere">Fasta everywhere</h2>
-<p>We ran our pipeline on one fasta file. How would nextflow handle 100 of them? To test that we need to duplicate the <code>tiny_v2.fasta</code> file:</p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb14-1" title="1"><span class="kw">for</span> <span class="ex">i</span> in <span class="dt">{1..100}</span></a>
-<a class="sourceLine" id="cb14-2" title="2"><span class="kw">do</span></a>
-<a class="sourceLine" id="cb14-3" title="3"><span class="fu">cp</span> data/tiny_dataset/fasta/tiny_v2.fasta data/tiny_dataset/fasta/tiny_v2_<span class="va">${i}</span>.fasta</a>
-<a class="sourceLine" id="cb14-4" title="4"><span class="kw">done</span></a></code></pre></div>
-<p>You can run your pipeline again and check the content of the folder <code>results/sampling</code>.</p>
-<p>Every <code>fasta_sampler</code> process write a <code>sample.fasta</code> file. We need to make the name of the output file dependent of the name of the input file.</p>
-<pre class="groovy"><code>output:
-file "*_sample.fasta" into fasta_sample
-
- script:
-"""
-head ${fasta} > ${fasta.baseName}_sample.fasta
-"""</code></pre>
-<p>Add this to your <code>src/fasta_sampler.nf</code> file with the WebIDE and commit it to your repository before pulling your modifications locally. You can run your pipeline again and check the content of the folder <code>results/sampling</code>.</p>
-<h1 id="build-your-own-rnaseq-pipeline">Build your own RNASeq pipeline</h1>
-<p>In this section you are going to build your own pipeline for RNASeq analysis from the code available in the <code>src/nf_modules</code> folder.</p>
-<h2 id="create-your-docker-containers">Create your Docker containers</h2>
-<p>For this practical, we are going to need the following tools:</p>
-<ul>
-<li>For Illumina adaptor removal: cutadapt</li>
-<li>For reads trimming by quality: UrQt</li>
-<li>For mapping and quantifying reads: BEDtools and Kallisto</li>
-</ul>
-<p>To initialize these tools, follow the <strong>Installing</strong> section of the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md">README.md</a> file.</p>
-<p><strong>If you are using a CBP computer don’t forget to clean up your docker containers at the end of the practical with the following commands:</strong></p>
-<div class="sourceCode" id="cb16"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb16-1" title="1"><span class="ex">docker</span> rm <span class="va">$(</span><span class="ex">docker</span> stop <span class="va">$(</span><span class="ex">docker</span> ps -aq<span class="va">))</span></a>
-<a class="sourceLine" id="cb16-2" title="2"><span class="ex">docker</span> rmi <span class="va">$(</span><span class="ex">docker</span> images -qf <span class="st">"dangling=true"</span><span class="va">)</span></a></code></pre></div>
-<h2 id="cutadapt">Cutadapt</h2>
-<p>The first step of the pipeline is to remove any Illumina adaptors left in your read files.</p>
-<p>Open the WebIDE and create a <code>src/RNASeq.nf</code> file. Browse for <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.nf">src/nf_modules/cutadapt/adaptor_removal_paired.nf</a>, this file contains examples for cutadapt. We are interested in the <em>Illumina adaptor removal</em>, <em>for paired-end data</em> section of the code. Copy this code in your pipeline and commit it.</p>
-<p>Compared to before, we have few new lines:</p>
-<pre class="groovy"><code>params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"</code></pre>
-<p>We declare a variable that contains the path of the fastq file to look for. The advantage of using <code>params.fastq</code> is that the option <code>--fastq</code> is now a parameter of your pipeline. Thus, you can call your pipeline with the <code>--fastq</code> option:</p>
-<div class="sourceCode" id="cb18"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb18-1" title="1"><span class="ex">./nextflow</span> src/RNASeq.nf --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span></a></code></pre></div>
-<pre class="groovy"><code>log.info "fastq files: ${params.fastq}"</code></pre>
-<p>This line simply displays the value of the variable</p>
-<pre class="groovy"><code>Channel
- .fromFilePairs( params.fastq )</code></pre>
-<p>As we are working with paired-end RNASeq data, we tell nextflow to send pairs of fastq in the <code>fastq_file</code> channel.</p>
-<h3 id="cutadapt.config">cutadapt.config</h3>
-<p>For the <code>fastq_sampler.nf</code> pipeline we used the command <code>head</code> present in most base UNIX systems. Here we want to use <code>cutadapt</code> which is not. Therefore, we have three main options:</p>
-<ul>
-<li>install cutadapt locally so nextflow can use it</li>
-<li>launch the process in a Docker container that has cutadapt installed</li>
-<li>launch the process with psmn while loading the correct module to have cutadapt available</li>
-</ul>
-<p>We are not going to use the first option which requires no configuration for nextflow but tedious tools installations. Instead, we are going to use existing <em>wrappers</em> and tell nextflow about it. This is what the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.config">src/nf_modules/cutadapt/adaptor_removal_paired.config</a> is used for.</p>
-<p>Copy the content of this config file to an <code>src/RNASeq.config</code> file. This file is structured in process blocks. Here we are only interested in configuring <code>adaptor_removal</code> process not <code>trimming</code> process. So you can remove the <code>trimming</code> block and commit it.</p>
-<p>You can test your pipeline with the following command:</p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb21-1" title="1"><span class="ex">./nextflow</span> src/RNASeq.nf -c src/RNASeq.config -profile docker --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span></a></code></pre></div>
-<h2 id="urqt">UrQt</h2>
-<p>The second step of the pipeline is to trim reads by quality.</p>
-<p>Browse for <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.nf">src/nf_modules/urqt/trimming_paired.nf</a>, this file contains examples for UrQt. We are interested in the <em>for paired-end data</em> section of the code. Copy the process section code in your pipeline and commit it.</p>
-<p>This code won’t work if you try to run it: the <code>fastq_file</code> channel is already consumed by the <code>adaptor_removal</code> process. In nextflow once a channel is used by a process, it ceases to exist. Moreover, we don’t want to trim the input fastq, we want to trim the fastq that comes from the <code>adaptor_removal</code> process.</p>
-<p>Therefore, you need to change the line:</p>
-<pre class="groovy"><code>set pair_id, file(reads) from fastq_files</code></pre>
-<p>In the <code>trimming</code> process to:</p>
-<pre class="groovy"><code>set pair_id, file(reads) from fastq_files_cut</code></pre>
-<p>The two processes are now connected by the channel <code>fastq_files_cut</code>.</p>
-<p>Add the content of the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.config">src/nf_modules/urqt/trimming_paired.config</a> file to your <code>src/RNASeq.config</code> file and commit it.</p>
-<p>You can test your pipeline.</p>
-<h2 id="bedtools">BEDtools</h2>
-<p>Kallisto need the sequences of the transcripts that need to be quantified. We are going to extract these sequences from the reference <code>data/tiny_dataset/fasta/tiny_v2.fasta</code> with the <code>bed</code> annotation <code>data/tiny_dataset/annot/tiny.bed</code>.</p>
-<p>You can copy to your <code>src/RNASeq.nf</code> file the content of <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.nf">src/nf_modules/bedtools/fasta_from_bed.nf</a> and to your <code>src/RNASeq.config</code> file the content of <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.config">src/nf_modules/bedtools/fasta_from_bed.config</a>.</p>
-<p>Commit your work and test your pipeline with the following command:</p>
-<div class="sourceCode" id="cb24"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb24-1" title="1"><span class="ex">./nextflow</span> src/RNASeq.nf -c src/RNASeq.config -profile docker --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span> --fasta <span class="st">"data/tiny_dataset/fasta/tiny_v2.fasta"</span> --bed <span class="st">"data/tiny_dataset/annot/tiny.bed"</span></a></code></pre></div>
-<h2 id="kallisto">Kallisto</h2>
-<p>Kallisto run in two steps: the indexation of the reference and the quantification on this index.</p>
-<p>You can copy to your <code>src/RNASeq.nf</code> file the content of the files <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.nf">src/nf_modules/kallisto/indexing.nf</a> and <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.nf">src/nf_modules/kallisto/mapping_paired.nf</a>. You can add to your file <code>src/RNASeq.config</code> file the content of the files <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.config">src/nf_modules/kallisto/indexing.config</a> and <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.config">src/nf_modules/kallisto/mapping_paired.config</a>.</p>
-<p>We are going to work with paired-end so only copy the relevant processes. The <code>index_fasta</code> process needs to take as input the output of your <code>fasta_from_bed</code> process. The <code>fastq</code> input of your <code>mapping_fastq</code> process needs to take as input the output of your <code>index_fasta</code> process and the <code>trimming</code> process.</p>
-<p>Commit your work and test your pipeline. You now have a RNASeq analysis pipeline that can run locally with Docker!</p>
-<h2 id="additional-nextflow-option">Additional nextflow option</h2>
-<p>With nextflow you can restart the computation of a pipeline and get a trace of the process with the following options:</p>
-<div class="sourceCode" id="cb25"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb25-1" title="1"> <span class="ex">-resume</span> -with-dag results/RNASeq_dag.pdf -with-timeline results/RNASeq_timeline</a></code></pre></div>
-<h1 id="run-your-rnaseq-pipeline-on-the-psmn">Run your RNASeq pipeline on the PSMN</h1>
-<p>First you need to connect to the PSMN:</p>
-<div class="sourceCode" id="cb26"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb26-1" title="1"><span class="ex">login@allo-psmn</span></a></code></pre></div>
-<p>Then once connected to <code>allo-psmn</code>, you can connect to <code>e5-2667v4comp1</code>:</p>
-<div class="sourceCode" id="cb27"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb27-1" title="1"><span class="ex">login@e5-2667v4comp1</span></a></code></pre></div>
-<h2 id="set-your-environment">Set your environment</h2>
-<p>Make the LBMC modules available to you:</p>
-<div class="sourceCode" id="cb28"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb28-1" title="1"><span class="fu">ln</span> -s /Xnfs/lbmcdb/common/modules/modulefiles ~/privatemodules</a>
-<a class="sourceLine" id="cb28-2" title="2"><span class="bu">echo</span> <span class="st">"module use ~/privatemodules"</span> <span class="op">>></span> .bashrc</a></code></pre></div>
-<p>Create and go to your <code>scratch</code> folder:</p>
-<div class="sourceCode" id="cb29"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb29-1" title="1"><span class="fu">mkdir</span> -p /scratch/<span class="op"><</span>login<span class="op">></span></a>
-<a class="sourceLine" id="cb29-2" title="2"><span class="bu">cd</span> /scratch/<span class="op"><</span>login<span class="op">></span></a>
-<a class="sourceLine" id="cb29-3" title="3"><span class="bu">echo</span> <span class="st">"module use ~/privatemodules"</span> <span class="op">>></span> .bashrc</a></code></pre></div>
-<p>Then you need to clone your pipeline and get the data:</p>
-<div class="sourceCode" id="cb30"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb30-1" title="1"><span class="fu">git</span> config --global http.sslVerify false</a>
-<a class="sourceLine" id="cb30-2" title="2"><span class="fu">git</span> clone https://gitlab.biologie.ens-lyon.fr/<span class="op"><</span>usr_name<span class="op">></span>/nextflow.git</a>
-<a class="sourceLine" id="cb30-3" title="3"><span class="bu">cd</span> nextflow/data</a>
-<a class="sourceLine" id="cb30-4" title="4"><span class="fu">git</span> clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git</a>
-<a class="sourceLine" id="cb30-5" title="5"><span class="bu">cd</span> ..</a></code></pre></div>
-<h2 id="run-nextflow">Run nextflow</h2>
-<p>As we don’t want nextflow to be killed in case of disconnection, we start by launching <code>tmux</code>. In case of deconnection, you can restore your session with the command <code>tmux a</code>.</p>
-<div class="sourceCode" id="cb31"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb31-1" title="1"><span class="ex">tmux</span></a>
-<a class="sourceLine" id="cb31-2" title="2"><span class="ex">module</span> load nextflow/0.28.2</a>
-<a class="sourceLine" id="cb31-3" title="3"><span class="ex">nextflow</span> src/RNASeq.nf -c src/RNASeq.config -profile psmn --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span> --fasta <span class="st">"data/tiny_dataset/fasta/tiny_v2.fasta"</span> --bed <span class="st">"data/tiny_dataset/annot/tiny.bed"</span> -w /scratch/<span class="op"><</span>login<span class="op">></span></a></code></pre></div>
-<p>To use the scratch for nextflow computations add the option :</p>
-<div class="sourceCode" id="cb32"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb32-1" title="1"><span class="ex">-w</span> /scratch/<span class="op"><</span>login<span class="op">></span></a></code></pre></div>
-<p>You just ran your pipeline on the PSMN!</p>
-</body>
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-</head>
-<body>
-<p>The Goal of this practical is to learn how to build your own pipeline with nextflow and using the tools already <em>wrapped</em>. For this we are going to build a small RNASeq analysis pipeline that should run the following steps:</p>
-<ul>
-<li>remove Illumina adaptors</li>
-<li>trim reads by quality</li>
-<li>build the index of a reference genome</li>
-<li>estimate the amount of RNA fragments mapping to the transcripts of this genome</li>
-</ul>
-<h1 id="initialize-your-own-project">Initialize your own project</h1>
-<p>You are going to build a pipeline for you or your team. So the first step is to create your own project.</p>
-<h2 id="forking">Forking</h2>
-<p>Instead of reinventing the wheel, you can use the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a> as a template. To easily do so, go to the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a> repository and click on the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/forks/new"><strong>fork</strong></a> button.</p>
-<figure>
-<img src="img/fork.png" alt="fork button" /><figcaption>fork button</figcaption>
-</figure>
-<p>In git, the <a href="https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project">action of forking</a> means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository (here <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a>) create a merge request. Merge requests are sent to the source repository to ask the maintainers to integrate modifications.</p>
-<figure>
-<img src="img/merge_request.png" alt="merge request button" /><figcaption>merge request button</figcaption>
-</figure>
-<h2 id="project-organisation">Project organisation</h2>
-<p>This project (and yours) follows the <a href="http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/ressources/good_practice_LBMC">guide of good practices for the LBMC</a></p>
-<p>You are now on the main page of your fork of the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a>. You can explore this project, all the code in it is under the CeCILL licence (in the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/LICENSE">LICENCE</a> file).</p>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md">README.md</a> file contains instructions to run your pipeline and test its installation.</p>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/CONTRIBUTING.md">CONTRIBUTING.md</a> file contains guidelines if you want to contribute to the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow">pipelines/nextflow</a> (making a merge request for example).</p>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/data">data</a> folder will be the place where you store the raw data for your analysis. The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/results">results</a> folder will be the place where you store the results of your analysis.</p>
-<blockquote>
-<p><strong>The content of <code>data</code> and <code>results</code> folders should never be saved on git.</strong></p>
-</blockquote>
-<p>The <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/doc">doc</a> folder contains the documentation of this practical course.</p>
-<p>And most interestingly for you, the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src">src</a> contains code to wrap tools. This folder contains two subdirectories. A <code>docker_modules</code>, a <code>nf_modules</code> and a <code>psmn_modules</code> folder.</p>
-<h3 id="docker_modules"><code>docker_modules</code></h3>
-<p>The <code>src/docker_modules</code> contains the code to wrap tools in <a href="https://www.docker.com/what-docker">Docker</a>. <a href="https://www.docker.com/what-docker">Docker</a> is a framework that allows you to execute software within <a href="https://www.docker.com/what-container">containers</a>. The <code>docker_modules</code> contains directory corresponding to tools and subdirectories corresponding to their version.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" title="1"><span class="fu">ls</span> -l src/docker_modules/</a>
-<a class="sourceLine" id="cb1-2" title="2"><span class="ex">rwxr-xr-x</span> 3 laurent _lpoperator 96 May 25 15:42 bedtools/</a>
-<a class="sourceLine" id="cb1-3" title="3"><span class="ex">drwxr-xr-x</span> 4 laurent _lpoperator 128 Jun 5 16:14 bowtie2/</a>
-<a class="sourceLine" id="cb1-4" title="4"><span class="ex">drwxr-xr-x</span> 3 laurent _lpoperator 96 May 25 15:42 fastqc/</a>
-<a class="sourceLine" id="cb1-5" title="5"><span class="ex">drwxr-xr-x</span> 4 laurent _lpoperator 128 Jun 5 16:14 htseq/</a></code></pre></div>
-<p>To each <code>tools/version</code> corresponds two files:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb2-1" title="1"><span class="fu">ls</span> -l src/docker_modules/bowtie2/2.3.4.1/</a>
-<a class="sourceLine" id="cb2-2" title="2"><span class="ex">-rw-r--r--</span> 1 laurent _lpoperator 283 Jun 5 15:07 Dockerfile</a>
-<a class="sourceLine" id="cb2-3" title="3"><span class="ex">-rwxr-xr-x</span> 1 laurent _lpoperator 79 Jun 5 16:18 docker_init.sh*</a></code></pre></div>
-<p>The <code>Dockerfile</code> is the <a href="https://www.docker.com/what-docker">Docker</a> recipe to create a <a href="https://www.docker.com/what-container">container</a> containing <code>Bowtie2</code> in its <code>2.3.4.1</code> version. And the <code>docker_init.sh</code> file is a small script to create the <a href="https://www.docker.com/what-container">container</a> from this recipe.</p>
-<p>By running this script you will be able to easily install tools in different versions on your personal computer and use it in your pipeline. Some of the advantages are:</p>
-<ul>
-<li>Whatever the computer, the installation and the results will be the same</li>
-<li>You can keep <a href="https://www.docker.com/what-container">container</a> for old version of tools and run it on new systems (science = reproducibility)</li>
-<li>You don’t have to bother with tedious installation procedures, somebody else already did the job and wrote a <code>Dockerfile</code>.</li>
-<li>You can easily keep <a href="https://www.docker.com/what-container">containers</a> for different version of the same tools.</li>
-</ul>
-<h3 id="psmn_modules"><code>psmn_modules</code></h3>
-<p>The <code>src/psmn_modules</code> folder is not really there. It’s a submodule of the project <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a>. To populate it locally you can use the following command:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb3-1" title="1"><span class="fu">git</span> submodule init</a></code></pre></div>
-<p>Like the <code>src/docker_modules</code> the <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a> project describe recipes to install tools and use them. The main difference is that you cannot use <a href="https://www.docker.com/what-docker">Docker</a> on the PSMN. Instead you have to use another framework <a href="http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules">Environment Module</a> which allows you to load modules for specific tools and version. The <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/README.md">README.md</a> file of the <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a> repository contains all the instruction to be able to load the modules maintained by the LBMC and present in the <a href="https://gitlab.biologie.ens-lyon.fr/PSMN/modules">PSMN/modules</a> repository.</p>
-<h3 id="nf_modules"><code>nf_modules</code></h3>
-<p>The <code>src/nf_modules</code> folder contains templates of <a href="https://www.nextflow.io/">nextflow</a> wrappers for the tools available in <a href="https://www.docker.com/what-docker">Docker</a> and <a href="http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:psmn">psmn</a>. The details of the <a href="https://www.nextflow.io/">nextflow</a> wrapper will be presented in the next section. Alongside the <code>.nf</code> and <code>.config</code> files, there is a <code>tests.sh</code> script to run test on the tool.</p>
-<h1 id="nextflow-pipeline">Nextflow pipeline</h1>
-<p>A pipeline is a succession of <strong>process</strong>. Each process has data input(s) and optional data output(s). Data flows are modeled as <strong>channels</strong>.</p>
-<h2 id="processes">Processes</h2>
-<p>Here is an example of <strong>process</strong>:</p>
-<pre class="groovy"><code>process sample_fasta {
- input:
-file fasta from fasta_file
-
- output:
-file "sample.fasta" into fasta_sample
-
- script:
-"""
-head ${fasta} > sample.fasta
-"""
-}</code></pre>
-<p>We have the process <code>sample_fasta</code> that takes a <code>fasta_file</code> <strong>channel</strong> as input and as output a <code>fasta_sample</code> <strong>channel</strong>. The process itself is defined in the <code>script:</code> block and within <code>"""</code>.</p>
-<pre class="groovy"><code>input:
-file fasta from fasta_file</code></pre>
-<p>When we zoom on the <code>input:</code> block we see that we define a variable <code>fasta</code> of type <code>file</code> from the <code>fasta_file</code> <strong>channel</strong>. This mean that groovy is going to write a file named as the content of the variable <code>fasta</code> in the root of the folder where <code>script:</code> is executed.</p>
-<pre class="groovy"><code>output:
-file "sample.fasta" into fasta_sample</code></pre>
-<p>At the end of the script, a file named <code>sample.fasta</code> is found in the root the folder where <code>script:</code> is executed and send into the <strong>channel</strong> <code>fasta_sample</code>.</p>
-<p>Using the WebIDE of Gitlab, create a file <code>src/fasta_sampler.nf</code> with this process and commit it to your repository.</p>
-<figure>
-<img src="img/webide.png" alt="webide" /><figcaption>webide</figcaption>
-</figure>
-<h2 id="channels">Channels</h2>
-<p>Why bother with channels? In the above example, the advantages of channels are not really clear. We could have just given the <code>fasta</code> file to the process. But what if we have many fasta files to process? What if we have sub processes to run on each of the sampled fasta files? Nextflow can easily deal with these problems with the help of channels.</p>
-<blockquote>
-<p><strong>Channels</strong> are streams of items that are emitted by a source and consumed by a process. A process with a channel as input will be run on every item send through the channel.</p>
-</blockquote>
-<pre class="groovy"><code>Channel
- .fromPath( "data/tiny_dataset/fasta/*.fasta" )
- .set { fasta_file }</code></pre>
-<p>Here we defined the channel <code>fasta_file</code> that is going to send every fasta file from the folder <code>data/tiny_dataset/fasta/</code> into the process that take it as input.</p>
-<p>Add the definition of the channel to the <code>src/fasta_sampler.nf</code> file and commit it to your repository.</p>
-<h2 id="run-your-pipeline-locally">Run your pipeline locally</h2>
-<p>After writing this first pipeline, you may want to test it. To do that, first clone your repository. To easily do that set the visibility level to <em>public</em> in the settings/General/Permissions page of your project.</p>
-<p>You can then run the following commands to download your project on your computer:</p>
-<p>If you are on a PSMN computer:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb8-1" title="1"><span class="ex">pip</span> install cutadapt=1.14</a>
-<a class="sourceLine" id="cb8-2" title="2"><span class="va">PATH=</span><span class="st">"/scratch/lmodolo/:</span><span class="va">$PATH</span><span class="st">"</span></a>
-<a class="sourceLine" id="cb8-3" title="3"><span class="fu">git</span> config --global http.sslVerify false</a></code></pre></div>
-<p>and then :</p>
-<blockquote>
-<p>Don’t forget to replace <em>https://gitlab.biologie.ens-lyon.fr/</em> by <em>gitlab_lbmc</em> if you are using your own computer</p>
-</blockquote>
-<div class="sourceCode" id="cb9"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb9-1" title="1"><span class="fu">git</span> clone https://gitlab.biologie.ens-lyon.fr/<span class="op"><</span>usr_name<span class="op">></span>/nextflow.git</a>
-<a class="sourceLine" id="cb9-2" title="2"><span class="bu">cd</span> nextflow</a>
-<a class="sourceLine" id="cb9-3" title="3"><span class="ex">src/install_nextflow.sh</span></a></code></pre></div>
-<p>We also need data to run our pipeline:</p>
-<pre><code>cd data
-git clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
-cd ..</code></pre>
-<p>We can run our pipeline with the following command:</p>
-<div class="sourceCode" id="cb11"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb11-1" title="1"><span class="ex">./nextflow</span> src/fasta_sampler.nf</a></code></pre></div>
-<h2 id="getting-your-results">Getting your results</h2>
-<p>Our pipeline seems to work but we don’t know where is the <code>sample.fasta</code>. To get results out of a process, we need to tell nextflow to write it somewhere (we may don’t need to get every intermediate file in our results).</p>
-<p>To do that we need to add the following line before the <code>input:</code> section:</p>
-<pre class="groovy"><code>publishDir "results/sampling/", mode: 'copy'</code></pre>
-<p>Every file described in the <code>output:</code> section will be copied from nextflow to the folder <code>results/sampling/</code>.</p>
-<p>Add this to your <code>src/fasta_sampler.nf</code> file with the WebIDE and commit to your repository. Pull your modifications locally with the command:</p>
-<div class="sourceCode" id="cb13"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb13-1" title="1"><span class="fu">git</span> pull origin master</a></code></pre></div>
-<p>You can run your pipeline again and check the content of the folder <code>results/sampling</code>.</p>
-<h2 id="fasta-everywhere">Fasta everywhere</h2>
-<p>We ran our pipeline on one fasta file. How would nextflow handle 100 of them? To test that we need to duplicate the <code>tiny_v2.fasta</code> file:</p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb14-1" title="1"><span class="kw">for</span> <span class="ex">i</span> in <span class="dt">{1..100}</span></a>
-<a class="sourceLine" id="cb14-2" title="2"><span class="kw">do</span></a>
-<a class="sourceLine" id="cb14-3" title="3"><span class="fu">cp</span> data/tiny_dataset/fasta/tiny_v2.fasta data/tiny_dataset/fasta/tiny_v2_<span class="va">${i}</span>.fasta</a>
-<a class="sourceLine" id="cb14-4" title="4"><span class="kw">done</span></a></code></pre></div>
-<p>You can run your pipeline again and check the content of the folder <code>results/sampling</code>.</p>
-<p>Every <code>fasta_sampler</code> process write a <code>sample.fasta</code> file. We need to make the name of the output file dependent of the name of the input file.</p>
-<pre class="groovy"><code>output:
-file "*_sample.fasta" into fasta_sample
-
- script:
-"""
-head ${fasta} > ${fasta.baseName}_sample.fasta
-"""</code></pre>
-<p>Add this to your <code>src/fasta_sampler.nf</code> file with the WebIDE and commit it to your repository before pulling your modifications locally. You can run your pipeline again and check the content of the folder <code>results/sampling</code>.</p>
-<h1 id="build-your-own-rnaseq-pipeline">Build your own RNASeq pipeline</h1>
-<p>In this section you are going to build your own pipeline for RNASeq analysis from the code available in the <code>src/nf_modules</code> folder.</p>
-<h2 id="create-your-docker-containers">Create your Docker containers</h2>
-<p>For this practical, we are going to need the following tools:</p>
-<ul>
-<li>For Illumina adaptor removal: cutadapt</li>
-<li>For reads trimming by quality: UrQt</li>
-<li>For mapping and quantifying reads: BEDtools and Kallisto</li>
-</ul>
-<p>To initialize these tools, follow the <strong>Installing</strong> section of the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md">README.md</a> file.</p>
-<p><strong>If you are using a CBP computer don’t forget to clean up your docker containers at the end of the practical with the following commands:</strong></p>
-<div class="sourceCode" id="cb16"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb16-1" title="1"><span class="ex">docker</span> rm <span class="va">$(</span><span class="ex">docker</span> stop <span class="va">$(</span><span class="ex">docker</span> ps -aq<span class="va">))</span></a>
-<a class="sourceLine" id="cb16-2" title="2"><span class="ex">docker</span> rmi <span class="va">$(</span><span class="ex">docker</span> images -qf <span class="st">"dangling=true"</span><span class="va">)</span></a></code></pre></div>
-<h2 id="cutadapt">Cutadapt</h2>
-<p>The first step of the pipeline is to remove any Illumina adaptors left in your read files.</p>
-<p>Open the WebIDE and create a <code>src/RNASeq.nf</code> file. Browse for <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.nf">src/nf_modules/cutadapt/adaptor_removal_paired.nf</a>, this file contains examples for cutadapt. We are interested in the <em>Illumina adaptor removal</em>, <em>for paired-end data</em> section of the code. Copy this code in your pipeline and commit it.</p>
-<p>Compared to before, we have few new lines:</p>
-<pre class="groovy"><code>params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"</code></pre>
-<p>We declare a variable that contains the path of the fastq file to look for. The advantage of using <code>params.fastq</code> is that the option <code>--fastq</code> is now a parameter of your pipeline. Thus, you can call your pipeline with the <code>--fastq</code> option:</p>
-<div class="sourceCode" id="cb18"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb18-1" title="1"><span class="ex">./nextflow</span> src/RNASeq.nf --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span></a></code></pre></div>
-<pre class="groovy"><code>log.info "fastq files: ${params.fastq}"</code></pre>
-<p>This line simply displays the value of the variable</p>
-<pre class="groovy"><code>Channel
- .fromFilePairs( params.fastq )</code></pre>
-<p>As we are working with paired-end RNASeq data, we tell nextflow to send pairs of fastq in the <code>fastq_file</code> channel.</p>
-<h3 id="cutadapt.config">cutadapt.config</h3>
-<p>For the <code>fastq_sampler.nf</code> pipeline we used the command <code>head</code> present in most base UNIX systems. Here we want to use <code>cutadapt</code> which is not. Therefore, we have three main options:</p>
-<ul>
-<li>install cutadapt locally so nextflow can use it</li>
-<li>launch the process in a Docker container that has cutadapt installed</li>
-<li>launch the process with psmn while loading the correct module to have cutadapt available</li>
-</ul>
-<p>We are not going to use the first option which requires no configuration for nextflow but tedious tools installations. Instead, we are going to use existing <em>wrappers</em> and tell nextflow about it. This is what the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.config">src/nf_modules/cutadapt/adaptor_removal_paired.config</a> is used for.</p>
-<p>Copy the content of this config file to an <code>src/RNASeq.config</code> file. This file is structured in process blocks. Here we are only interested in configuring <code>adaptor_removal</code> process not <code>trimming</code> process. So you can remove the <code>trimming</code> block and commit it.</p>
-<p>You can test your pipeline with the following command:</p>
-<div class="sourceCode" id="cb21"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb21-1" title="1"><span class="ex">./nextflow</span> src/RNASeq.nf -c src/RNASeq.config -profile docker --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span></a></code></pre></div>
-<h2 id="urqt">UrQt</h2>
-<p>The second step of the pipeline is to trim reads by quality.</p>
-<p>Browse for <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.nf">src/nf_modules/urqt/trimming_paired.nf</a>, this file contains examples for UrQt. We are interested in the <em>for paired-end data</em> section of the code. Copy the process section code in your pipeline and commit it.</p>
-<p>This code won’t work if you try to run it: the <code>fastq_file</code> channel is already consumed by the <code>adaptor_removal</code> process. In nextflow once a channel is used by a process, it ceases to exist. Moreover, we don’t want to trim the input fastq, we want to trim the fastq that comes from the <code>adaptor_removal</code> process.</p>
-<p>Therefore, you need to change the line:</p>
-<pre class="groovy"><code>set pair_id, file(reads) from fastq_files</code></pre>
-<p>In the <code>trimming</code> process to:</p>
-<pre class="groovy"><code>set pair_id, file(reads) from fastq_files_cut</code></pre>
-<p>The two processes are now connected by the channel <code>fastq_files_cut</code>.</p>
-<p>Add the content of the <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.config">src/nf_modules/urqt/trimming_paired.config</a> file to your <code>src/RNASeq.config</code> file and commit it.</p>
-<p>You can test your pipeline.</p>
-<h2 id="bedtools">BEDtools</h2>
-<p>Kallisto need the sequences of the transcripts that need to be quantified. We are going to extract these sequences from the reference <code>data/tiny_dataset/fasta/tiny_v2.fasta</code> with the <code>bed</code> annotation <code>data/tiny_dataset/annot/tiny.bed</code>.</p>
-<p>You can copy to your <code>src/RNASeq.nf</code> file the content of <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.nf">src/nf_modules/bedtools/fasta_from_bed.nf</a> and to your <code>src/RNASeq.config</code> file the content of <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.config">src/nf_modules/bedtools/fasta_from_bed.config</a>.</p>
-<p>Commit your work and test your pipeline with the following command:</p>
-<div class="sourceCode" id="cb24"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb24-1" title="1"><span class="ex">./nextflow</span> src/RNASeq.nf -c src/RNASeq.config -profile docker --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span> --fasta <span class="st">"data/tiny_dataset/fasta/tiny_v2.fasta"</span> --bed <span class="st">"data/tiny_dataset/annot/tiny.bed"</span></a></code></pre></div>
-<h2 id="kallisto">Kallisto</h2>
-<p>Kallisto run in two steps: the indexation of the reference and the quantification on this index.</p>
-<p>You can copy to your <code>src/RNASeq.nf</code> file the content of the files <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.nf">src/nf_modules/kallisto/indexing.nf</a> and <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.nf">src/nf_modules/kallisto/mapping_paired.nf</a>. You can add to your file <code>src/RNASeq.config</code> file the content of the files <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.config">src/nf_modules/kallisto/indexing.config</a> and <a href="https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.config">src/nf_modules/kallisto/mapping_paired.config</a>.</p>
-<p>We are going to work with paired-end so only copy the relevant processes. The <code>index_fasta</code> process needs to take as input the output of your <code>fasta_from_bed</code> process. The <code>fastq</code> input of your <code>mapping_fastq</code> process needs to take as input the output of your <code>index_fasta</code> process and the <code>trimming</code> process.</p>
-<p>Commit your work and test your pipeline. You now have a RNASeq analysis pipeline that can run locally with Docker!</p>
-<h2 id="additional-nextflow-option">Additional nextflow option</h2>
-<p>With nextflow you can restart the computation of a pipeline and get a trace of the process with the following options:</p>
-<div class="sourceCode" id="cb25"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb25-1" title="1"> <span class="ex">-resume</span> -with-dag results/RNASeq_dag.pdf -with-timeline results/RNASeq_timeline</a></code></pre></div>
-<h1 id="run-your-rnaseq-pipeline-on-the-psmn">Run your RNASeq pipeline on the PSMN</h1>
-<p>First you need to connect to the PSMN:</p>
-<div class="sourceCode" id="cb26"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb26-1" title="1"><span class="ex">login@allo-psmn</span></a></code></pre></div>
-<p>Then once connected to <code>allo-psmn</code>, you can connect to <code>e5-2667v4comp1</code>:</p>
-<div class="sourceCode" id="cb27"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb27-1" title="1"><span class="ex">login@e5-2667v4comp1</span></a></code></pre></div>
-<h2 id="set-your-environment">Set your environment</h2>
-<p>Make the LBMC modules available to you:</p>
-<div class="sourceCode" id="cb28"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb28-1" title="1"><span class="fu">ln</span> -s /Xnfs/lbmcdb/common/modules/modulefiles ~/privatemodules</a>
-<a class="sourceLine" id="cb28-2" title="2"><span class="bu">echo</span> <span class="st">"module use ~/privatemodules"</span> <span class="op">>></span> .bashrc</a></code></pre></div>
-<p>Create and go to your <code>scratch</code> folder:</p>
-<div class="sourceCode" id="cb29"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb29-1" title="1"><span class="fu">mkdir</span> -p /scratch/<span class="op"><</span>login<span class="op">></span></a>
-<a class="sourceLine" id="cb29-2" title="2"><span class="bu">cd</span> /scratch/<span class="op"><</span>login<span class="op">></span></a>
-<a class="sourceLine" id="cb29-3" title="3"><span class="bu">echo</span> <span class="st">"module use ~/privatemodules"</span> <span class="op">>></span> .bashrc</a></code></pre></div>
-<p>Then you need to clone your pipeline and get the data:</p>
-<div class="sourceCode" id="cb30"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb30-1" title="1"><span class="fu">git</span> config --global http.sslVerify false</a>
-<a class="sourceLine" id="cb30-2" title="2"><span class="fu">git</span> clone https://gitlab.biologie.ens-lyon.fr/<span class="op"><</span>usr_name<span class="op">></span>/nextflow.git</a>
-<a class="sourceLine" id="cb30-3" title="3"><span class="bu">cd</span> nextflow/data</a>
-<a class="sourceLine" id="cb30-4" title="4"><span class="fu">git</span> clone https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git</a>
-<a class="sourceLine" id="cb30-5" title="5"><span class="bu">cd</span> ..</a></code></pre></div>
-<h2 id="run-nextflow">Run nextflow</h2>
-<p>As we don’t want nextflow to be killed in case of disconnection, we start by launching <code>tmux</code>. In case of deconnection, you can restore your session with the command <code>tmux a</code>.</p>
-<div class="sourceCode" id="cb31"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb31-1" title="1"><span class="ex">tmux</span></a>
-<a class="sourceLine" id="cb31-2" title="2"><span class="ex">module</span> load nextflow/0.28.2</a>
-<a class="sourceLine" id="cb31-3" title="3"><span class="ex">nextflow</span> src/RNASeq.nf -c src/RNASeq.config -profile psmn --fastq <span class="st">"data/tiny_dataset/fastq/*_R{1,2}.fastq"</span> --fasta <span class="st">"data/tiny_dataset/fasta/tiny_v2.fasta"</span> --bed <span class="st">"data/tiny_dataset/annot/tiny.bed"</span> -w /scratch/<span class="op"><</span>login<span class="op">></span></a></code></pre></div>
-<p>To use the scratch for nextflow computations add the option :</p>
-<div class="sourceCode" id="cb32"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb32-1" title="1"><span class="ex">-w</span> /scratch/<span class="op"><</span>login<span class="op">></span></a></code></pre></div>
-<p>You just ran your pipeline on the PSMN!</p>
-</body>
-</html>
diff --git a/results/.gitignore b/results/.gitignore
index 72e8ffc0db8aad71a934dd11e5968bd5109e54b4..8a8feafc11a33ce80e2a8572af3ad268ee8b73eb 100644
--- a/results/.gitignore
+++ b/results/.gitignore
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
*
diff --git a/src/.docker_modules/CITE-seq-Count/1.4.5/Dockerfile b/src/.docker_modules/CITE-seq-Count/1.4.5/Dockerfile
index 1bba8944976a3f5a2013b2840d0b813424bed003..aa9e22d303789aeee00ab2d0b18711505dc10225 100644
--- a/src/.docker_modules/CITE-seq-Count/1.4.5/Dockerfile
+++ b/src/.docker_modules/CITE-seq-Count/1.4.5/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:22.04
ENV CITESEQ_VERSION=1.4.5
diff --git a/src/.docker_modules/CITE-seq-Count/1.4.5/docker_init.sh b/src/.docker_modules/CITE-seq-Count/1.4.5/docker_init.sh
index 99c3131549e952ca806eababc6645068c1e26f7b..c644c6667b1275a454ecbcbe39382793c3484306 100755
--- a/src/.docker_modules/CITE-seq-Count/1.4.5/docker_init.sh
+++ b/src/.docker_modules/CITE-seq-Count/1.4.5/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/cite_seq_count:1.4.5
docker build src/.docker_modules/CITE-seq-Count/1.4.5 -t 'lbmc/cite_seq_count:1.4.5'
docker push lbmc/cite_seq_count:1.4.5
diff --git a/src/.docker_modules/CITE-seq-Count/1.5.0/Dockerfile b/src/.docker_modules/CITE-seq-Count/1.5.0/Dockerfile
index 13fcf147ec7b30eecc2582fdd4be670ce71dce1e..f0ac74ec0cb4ca3951af7121fd4b1255239824ff 100644
--- a/src/.docker_modules/CITE-seq-Count/1.5.0/Dockerfile
+++ b/src/.docker_modules/CITE-seq-Count/1.5.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:22.04
ENV PACKAGES procps locales gcc libstdc++-10-dev libcurl4 libc6 python3 python3-pip python3-dev git
diff --git a/src/.docker_modules/CITE-seq-Count/1.5.0/docker_init.sh b/src/.docker_modules/CITE-seq-Count/1.5.0/docker_init.sh
index 419af5e7f011cc800cd0c7ef47e0d1363732302e..aad0b39f8066d6afd17ee97272474e03f4b4554d 100755
--- a/src/.docker_modules/CITE-seq-Count/1.5.0/docker_init.sh
+++ b/src/.docker_modules/CITE-seq-Count/1.5.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/cite_seq_count:1.5.0
docker build src/.docker_modules/CITE-seq-Count/1.5.0 -t 'lbmc/cite_seq_count:1.5.0'
docker push lbmc/cite_seq_count:1.5.0
diff --git a/src/.docker_modules/agat/0.8.0/Dockerfile b/src/.docker_modules/agat/0.8.0/Dockerfile
index 4325fc36b153587a048a205ad247eafc5dac2d94..1aef4a1a3e3602f66caab0ad69c404da38b86047 100644
--- a/src/.docker_modules/agat/0.8.0/Dockerfile
+++ b/src/.docker_modules/agat/0.8.0/Dockerfile
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0
\ No newline at end of file
diff --git a/src/.docker_modules/agat/0.8.0/docker_init.sh b/src/.docker_modules/agat/0.8.0/docker_init.sh
index ef8ca5cf34c9f47b0defa7874e66d48e41a09f26..8191ce9d4a5515b24507cf92c74adb5b8bee7345 100755
--- a/src/.docker_modules/agat/0.8.0/docker_init.sh
+++ b/src/.docker_modules/agat/0.8.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/agat:0.8.0
# docker build src/.docker_modules/agat/0.8.0 -t 'lbmc/agat:0.8.0'
# docker push lbmc/agat:0.8.0
diff --git a/src/.docker_modules/alntools/dd96682/Dockerfile b/src/.docker_modules/alntools/dd96682/Dockerfile
index 8bd4d05acee40478d3d0f9a79bc6dbd1c0789bd5..6828d83a8d3826ec625fbb5eb2f85fb6c36f3cee 100644
--- a/src/.docker_modules/alntools/dd96682/Dockerfile
+++ b/src/.docker_modules/alntools/dd96682/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-buster as build
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/alntools/dd96682/docker_init.sh b/src/.docker_modules/alntools/dd96682/docker_init.sh
index da1f1c97c94d6238ad520ebd7c97f5aa1e35f81f..1c4b92b95441e1a4eae55f965324c38bf19d6244 100755
--- a/src/.docker_modules/alntools/dd96682/docker_init.sh
+++ b/src/.docker_modules/alntools/dd96682/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/alntools:dd96682
# docker build src/.docker_modules/alntools/dd96682 -t 'lbmc/alntools:dd96682'
# docker push lbmc/alntools:dd96682
diff --git a/src/.docker_modules/bamutils/1.0.14/Dockerfile b/src/.docker_modules/bamutils/1.0.14/Dockerfile
index 9a116c6d442d99a997f1d9f5ada95a46e5366ab1..f246ae00b116f04c00c508737b2e5dc60a756a6f 100644
--- a/src/.docker_modules/bamutils/1.0.14/Dockerfile
+++ b/src/.docker_modules/bamutils/1.0.14/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bamutils/1.0.14/docker_init.sh b/src/.docker_modules/bamutils/1.0.14/docker_init.sh
index d89d2e5fb631378ef05003d270b44eedc5d67249..d748c48b9f90293367339461fe36ce02a99518eb 100755
--- a/src/.docker_modules/bamutils/1.0.14/docker_init.sh
+++ b/src/.docker_modules/bamutils/1.0.14/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bamutils:1.0.14
# docker build src/.docker_modules/bamutils/1.0.14 -t 'lbmc/bamutils:1.0.14'
# docker push lbmc/bamutils:1.0.14
diff --git a/src/.docker_modules/bcftools/1.7/Dockerfile b/src/.docker_modules/bcftools/1.7/Dockerfile
index b602f187b41a8d54429b06ca45822482292ed68a..bc386878609e89221d6d8af269161f5354df083e 100644
--- a/src/.docker_modules/bcftools/1.7/Dockerfile
+++ b/src/.docker_modules/bcftools/1.7/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bcftools/1.7/docker_init.sh b/src/.docker_modules/bcftools/1.7/docker_init.sh
index 55cab9902c35693f4876b09a650665ebd57bcbb8..50b1f42359a8e4ac40425e93803a7f04ea31af99 100755
--- a/src/.docker_modules/bcftools/1.7/docker_init.sh
+++ b/src/.docker_modules/bcftools/1.7/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bcftools:1.7
# docker build src/.docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
# docker push lbmc/bcftools:1.7
diff --git a/src/.docker_modules/bedops/2.4.39/Dockerfile b/src/.docker_modules/bedops/2.4.39/Dockerfile
index 2586c39b0c8f6fc0be6f145b0e72419c9c62f300..9fe3a46088b347f152ee9191988cd0b0e6e86438 100644
--- a/src/.docker_modules/bedops/2.4.39/Dockerfile
+++ b/src/.docker_modules/bedops/2.4.39/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/bedops:2.4.39--hc9558a2_0
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bedops/2.4.39/docker_init.sh b/src/.docker_modules/bedops/2.4.39/docker_init.sh
index 0c1ff388e2f37895999e0a868b450607e17598f1..cf488f86deb1f554d2c51d681748e52ea7b640d1 100755
--- a/src/.docker_modules/bedops/2.4.39/docker_init.sh
+++ b/src/.docker_modules/bedops/2.4.39/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bedops:2.4.39
# docker build src/.docker_modules/bedops/2.4.39 -t 'lbmc/bedops:2.4.39'
# docker push lbmc/bedops:2.4.39
diff --git a/src/.docker_modules/bedtools/2.25.0/Dockerfile b/src/.docker_modules/bedtools/2.25.0/Dockerfile
index 73be9c631be18e86b98ba3098275a269b4171650..4c451d044e9a32938062d7d1d0a3437144e1f844 100644
--- a/src/.docker_modules/bedtools/2.25.0/Dockerfile
+++ b/src/.docker_modules/bedtools/2.25.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:16.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bedtools/2.25.0/docker_init.sh b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
index 750ceb54c4f7bf601f24f86ad4203d87cdf84b2a..9e4d4d6796b7f16e468eaae39f8b0d47ba61a265 100755
--- a/src/.docker_modules/bedtools/2.25.0/docker_init.sh
+++ b/src/.docker_modules/bedtools/2.25.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bedtools:2.25.0
# docker build src/.docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'
# docker push lbmc/bedtools:2.25.0
diff --git a/src/.docker_modules/bedtools/2.30.0/Dockerfile b/src/.docker_modules/bedtools/2.30.0/Dockerfile
index e41c1f0f50e6e6c561bbdbfc059bd535bc8ad172..f25e37e60cd32496c476862f2e56be51e757cbb6 100644
--- a/src/.docker_modules/bedtools/2.30.0/Dockerfile
+++ b/src/.docker_modules/bedtools/2.30.0/Dockerfile
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1
\ No newline at end of file
diff --git a/src/.docker_modules/bedtools/2.30.0/docker_init.sh b/src/.docker_modules/bedtools/2.30.0/docker_init.sh
index b23fa27ee4e668610dca9da740fa53dbdc18e3db..6455c723930a80455b7c9896af9fbe06752a7276 100755
--- a/src/.docker_modules/bedtools/2.30.0/docker_init.sh
+++ b/src/.docker_modules/bedtools/2.30.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bedtools:2.30.0
docker build src/.docker_modules/bedtools/2.30.0 -t 'lbmc/bedtools:2.30.0'
docker push lbmc/bedtools:2.30.0
diff --git a/src/.docker_modules/bioawk/1.0/Dockerfile b/src/.docker_modules/bioawk/1.0/Dockerfile
index f7ca9803e60926ed90bce0abfe4cf7af90d72672..b4eeb42825515d0480087c6f19ae13d2ea726653 100644
--- a/src/.docker_modules/bioawk/1.0/Dockerfile
+++ b/src/.docker_modules/bioawk/1.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bioawk/1.0/docker_init.sh b/src/.docker_modules/bioawk/1.0/docker_init.sh
index 830fcf6bc977e70746fbfcc5e8f15e948cbf2773..86edc50b4f61e3a632e8d1ec1002d0f60a63054e 100755
--- a/src/.docker_modules/bioawk/1.0/docker_init.sh
+++ b/src/.docker_modules/bioawk/1.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bioawk:1.0
# docker build src/.docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
# docker push lbmc/bioawk:1.0
diff --git a/src/.docker_modules/bioconvert/0.4.0/Dockerfile b/src/.docker_modules/bioconvert/0.4.0/Dockerfile
index 5c05ff6f54610d2df6839e6e4a2a21c2e68e0845..5b1826b1803adf2cd65b992b2968477b25090388 100644
--- a/src/.docker_modules/bioconvert/0.4.0/Dockerfile
+++ b/src/.docker_modules/bioconvert/0.4.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM bioconvert/bioconvert:test
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bioconvert/0.4.0/docker_init.sh b/src/.docker_modules/bioconvert/0.4.0/docker_init.sh
index 0323c1bcf3645907796a93f5318849675d821977..f34c1227cf8d8b80ef06c35a3b4ff7f942a0b3b2 100755
--- a/src/.docker_modules/bioconvert/0.4.0/docker_init.sh
+++ b/src/.docker_modules/bioconvert/0.4.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bioconvert:0.4.0
# docker build src/.docker_modules/bioconvert/0.4.0 -t 'lbmc/bioconvert:0.4.0'
# docker push lbmc/bioconvert:0.4.0
diff --git a/src/.docker_modules/bioconvert/0.4.3/Dockerfile b/src/.docker_modules/bioconvert/0.4.3/Dockerfile
index eb4dc3d0b625a93eb5b0ce5506956e8ad39aabbc..82a279eddd74655ce56b9d6d863f9c0b67d48c9e 100644
--- a/src/.docker_modules/bioconvert/0.4.3/Dockerfile
+++ b/src/.docker_modules/bioconvert/0.4.3/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM conda/miniconda3
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bioconvert/0.4.3/docker_init.sh b/src/.docker_modules/bioconvert/0.4.3/docker_init.sh
index cbc76d9b9306c06fb1d19f460a989979f974a59a..ec927874b9dcd9677fe55dcc8ad93e53371ba232 100755
--- a/src/.docker_modules/bioconvert/0.4.3/docker_init.sh
+++ b/src/.docker_modules/bioconvert/0.4.3/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bioconvert:0.4.3
# docker build src/.docker_modules/bioconvert/0.4.3 -t 'lbmc/bioconvert:0.4.3'
# docker push lbmc/bioconvert:0.4.3
diff --git a/src/.docker_modules/bowtie/1.2.2/Dockerfile b/src/.docker_modules/bowtie/1.2.2/Dockerfile
index 128e68acde94e20c03130a0a3551978231f7a9cd..8e163d965ccc3c8fbc9dda3134df7b849f4a0322 100644
--- a/src/.docker_modules/bowtie/1.2.2/Dockerfile
+++ b/src/.docker_modules/bowtie/1.2.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bowtie/1.2.2/docker_init.sh b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
index 5bf220b3fc4fc30eb4e4f12f6f9f49426fc23273..bde585cda14c294ef39dd9a7a370a172761ee28c 100755
--- a/src/.docker_modules/bowtie/1.2.2/docker_init.sh
+++ b/src/.docker_modules/bowtie/1.2.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bowtie:1.2.2
# docker build src/.docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
# docker push lbmc/bowtie:1.2.2
diff --git a/src/.docker_modules/bowtie2/2.3.4.1/Dockerfile b/src/.docker_modules/bowtie2/2.3.4.1/Dockerfile
index 0f4ac75e48b5390714a22765c93939b72650b47e..25da8db4c77130481d867c9dbe16dd3d5973b9d6 100644
--- a/src/.docker_modules/bowtie2/2.3.4.1/Dockerfile
+++ b/src/.docker_modules/bowtie2/2.3.4.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
index 266039364df3288b7d69499946e7c5bb2f5958b3..6104886db32f595c19fc90a93afd103e02e8ca9b 100755
--- a/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
+++ b/src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bowtie2:2.3.4.1
# docker build src/.docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
# docker push lbmc/bowtie2:2.3.4.1
diff --git a/src/.docker_modules/bwa/0.7.17/Dockerfile b/src/.docker_modules/bwa/0.7.17/Dockerfile
index b5b5859a8f29564c5f260a094890223d4f04ebda..8c5476c8e76ebc9fe9d3202e6d68bd11b01aa007 100644
--- a/src/.docker_modules/bwa/0.7.17/Dockerfile
+++ b/src/.docker_modules/bwa/0.7.17/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM lbmc/samtools:1.11
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/bwa/0.7.17/docker_init.sh b/src/.docker_modules/bwa/0.7.17/docker_init.sh
index d50fafd812b26362b73b9e66672eadb65820e172..4c4a02922ccf45ced644ef0ff74aeac90e235cfa 100755
--- a/src/.docker_modules/bwa/0.7.17/docker_init.sh
+++ b/src/.docker_modules/bwa/0.7.17/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/bwa:0.7.17
# docker build src/.docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
# docker push lbmc/bwa:0.7.17
diff --git a/src/.docker_modules/canu/1.6/Dockerfile b/src/.docker_modules/canu/1.6/Dockerfile
index 66a55ef7ef5a6cc4ed048ee1a2494afd9877aa43..81cb85f758439475355c560192e8e4b12ff0cdf6 100644
--- a/src/.docker_modules/canu/1.6/Dockerfile
+++ b/src/.docker_modules/canu/1.6/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/canu/1.6/docker_init.sh b/src/.docker_modules/canu/1.6/docker_init.sh
index 58df472854b9345495433f14edc17504c918ead8..9cb093086e194c7ddc64bd75c321c20cdafc8e01 100755
--- a/src/.docker_modules/canu/1.6/docker_init.sh
+++ b/src/.docker_modules/canu/1.6/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/canu:1.6
# docker build src/.docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
# docker push lbmc/canu:1.6
diff --git a/src/.docker_modules/cellphonedb/3.0.0/Dockerfile b/src/.docker_modules/cellphonedb/3.0.0/Dockerfile
index 18e7cf712d67b5a4cf8998915212d236e38d8491..33fd060811610b7cc4965dc2b2d92a921fd4232a 100644
--- a/src/.docker_modules/cellphonedb/3.0.0/Dockerfile
+++ b/src/.docker_modules/cellphonedb/3.0.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.7-slim
ENV RPY2_CFFI_MODE=ABI
diff --git a/src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini.license b/src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile b/src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile
index 25b936ad249c9f0fd6003c503e7856c3a66e3435..3808da712f0225778dab27ec278b1c3bf8196f27 100644
--- a/src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile
+++ b/src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM postgres:9.6
ENV POSTGRES_PASSWORD root
diff --git a/src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh b/src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh
index 9b8cd443032f5a201190956c9ff1031689931842..144cbcc7ae19c16768f64387f151ec6ca2cfec57 100755
--- a/src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh
+++ b/src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh
@@ -1,3 +1,7 @@
#!/bin/bash
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
exec uwsgi --ini cellphonedb.ini --log-master
diff --git a/src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt.license b/src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/src/.docker_modules/cellphonedb/3.0.0/requirements.txt.license b/src/.docker_modules/cellphonedb/3.0.0/requirements.txt.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/requirements.txt.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/src/.docker_modules/clustalo/1.2.4/Dockerfile b/src/.docker_modules/clustalo/1.2.4/Dockerfile
index 52d6c748bdcdbd9a96b41da301a6d7d85262d53b..f53d3d405c76ab9dd1142f27be6863508f1b0def 100644
--- a/src/.docker_modules/clustalo/1.2.4/Dockerfile
+++ b/src/.docker_modules/clustalo/1.2.4/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:stretch-slim
ENV CLUSTALO_VERSION=1.2.4-1
diff --git a/src/.docker_modules/clustalo/1.2.4/docker_init.sh b/src/.docker_modules/clustalo/1.2.4/docker_init.sh
index 39addb3dcef0764c471348066ee75441aaa6df85..df07b979bb97258b5e9138207972833755d68b1c 100755
--- a/src/.docker_modules/clustalo/1.2.4/docker_init.sh
+++ b/src/.docker_modules/clustalo/1.2.4/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/clustalo:1.2.4
# docker build src/.docker_modules/clustalo/1.2.4 -t 'lbmc/clustalo:1.2.4'
# docker push lbmc/clustalo:1.2.4
diff --git a/src/.docker_modules/crossmap/0.4.1/Dockerfile b/src/.docker_modules/crossmap/0.4.1/Dockerfile
index bc988bb81d9f6fb83699092f8c68c5b476489a94..64ae29754da6f85ae95c822dd9943e3441b6d12d 100644
--- a/src/.docker_modules/crossmap/0.4.1/Dockerfile
+++ b/src/.docker_modules/crossmap/0.4.1/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/crossmap:0.4.1--pyh5ca1d4c_0
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/crossmap/0.4.1/docker_init.sh b/src/.docker_modules/crossmap/0.4.1/docker_init.sh
index a85ae11e491655126a71ad0ea4ac214d7d451209..385ff00d8fef8d5143df4c6be139fb1aca5d9142 100755
--- a/src/.docker_modules/crossmap/0.4.1/docker_init.sh
+++ b/src/.docker_modules/crossmap/0.4.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/crossmap:0.4.1
# docker build src/.docker_modules/crossmap/0.4.1/ -t 'lbmc/crossmap:0.4.1'
# docker push lbmc/crossmap:0.4.1
diff --git a/src/.docker_modules/cutadapt/1.14/Dockerfile b/src/.docker_modules/cutadapt/1.14/Dockerfile
index 35d23b7b235d3ad1e611af9287c92d9147f8e440..c969937c738f25fea4cd539d234bfed46e5655ae 100644
--- a/src/.docker_modules/cutadapt/1.14/Dockerfile
+++ b/src/.docker_modules/cutadapt/1.14/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.8
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/cutadapt/1.14/docker_init.sh b/src/.docker_modules/cutadapt/1.14/docker_init.sh
index 8febfd80bdfc6df62a59bdb4d1a1a136e3ac646e..c5aec167a04f6c0f9dc68f0c316a0bda566347d7 100755
--- a/src/.docker_modules/cutadapt/1.14/docker_init.sh
+++ b/src/.docker_modules/cutadapt/1.14/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/cutadapt:1.14
# docker build src/.docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
# docker push lbmc/cutadapt:1.14
diff --git a/src/.docker_modules/cutadapt/1.15/Dockerfile b/src/.docker_modules/cutadapt/1.15/Dockerfile
index 96bbd20ded423656458885b2522348711a838e97..f74ec0dd6b94f44842093c8a6848147c83643eae 100644
--- a/src/.docker_modules/cutadapt/1.15/Dockerfile
+++ b/src/.docker_modules/cutadapt/1.15/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.8
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/cutadapt/1.15/docker_init.sh b/src/.docker_modules/cutadapt/1.15/docker_init.sh
index 5f5b3c7779dfd637d93c3045d933767b81836707..2b84012eb0fcb3e40faf99f43bf590955597fe35 100755
--- a/src/.docker_modules/cutadapt/1.15/docker_init.sh
+++ b/src/.docker_modules/cutadapt/1.15/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/cutadapt:1.15
# docker build src/.docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
# docker push lbmc/cutadapt:1.15
diff --git a/src/.docker_modules/cutadapt/2.1/Dockerfile b/src/.docker_modules/cutadapt/2.1/Dockerfile
index cb394b2f6b4c6f1256b71e2d62520e714b411b99..e26e277101ca4f9b63256817f80b8f2d48eccab7 100644
--- a/src/.docker_modules/cutadapt/2.1/Dockerfile
+++ b/src/.docker_modules/cutadapt/2.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.8
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/cutadapt/2.1/docker_init.sh b/src/.docker_modules/cutadapt/2.1/docker_init.sh
index 2b631f0f4c2799971f9490dc3df0f264019c1296..50b66847c54550fec68411e2799814e47363c85d 100755
--- a/src/.docker_modules/cutadapt/2.1/docker_init.sh
+++ b/src/.docker_modules/cutadapt/2.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/cutadapt:2.1
# docker build src/.docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
# docker push lbmc/cutadapt:2.1
diff --git a/src/.docker_modules/danpos3/2f7f223/Dockerfile b/src/.docker_modules/danpos3/2f7f223/Dockerfile
index f9b4f63308d3839f335c8ca128e920c669660432..e0a8abfcdc37a371d0a77e0eced26e15638731c9 100644
--- a/src/.docker_modules/danpos3/2f7f223/Dockerfile
+++ b/src/.docker_modules/danpos3/2f7f223/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:20.04
ENV DANPOS_VERSION="2f7f223"
diff --git a/src/.docker_modules/danpos3/2f7f223/docker_init.sh b/src/.docker_modules/danpos3/2f7f223/docker_init.sh
index 9c59d3e259e4e1ef28466794b0ef5210190de652..a1196e6481b378de6c6cc0e78b46b779888ad109 100755
--- a/src/.docker_modules/danpos3/2f7f223/docker_init.sh
+++ b/src/.docker_modules/danpos3/2f7f223/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/danpos3:2f7f223
# docker build src/.docker_modules/danpos3/2f7f223 -t 'lbmc/danpos3:2f7f223'
# docker push lbmc/danpos3:2f7f223
diff --git a/src/.docker_modules/deeptools/3.0.2/Dockerfile b/src/.docker_modules/deeptools/3.0.2/Dockerfile
index 1d42cc9362faca77200117770ccb13dba10a1fe0..0ab63dd46f6cac2d19a219861a7f6fece372aae6 100644
--- a/src/.docker_modules/deeptools/3.0.2/Dockerfile
+++ b/src/.docker_modules/deeptools/3.0.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:stretch
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/deeptools/3.0.2/docker_init.sh b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
index 73ce8857ba40e1fe5b6c0b287e652a644738f987..50b49ef47e6ae4397103838e2a2fd8aaf006bb0d 100755
--- a/src/.docker_modules/deeptools/3.0.2/docker_init.sh
+++ b/src/.docker_modules/deeptools/3.0.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/deeptools:3.0.2
# docker build src/.docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
# docker push lbmc/deeptools:3.0.2
diff --git a/src/.docker_modules/deeptools/3.1.1/Dockerfile b/src/.docker_modules/deeptools/3.1.1/Dockerfile
index 2e84a709cd0078765070d284e5119e236b251283..47e8e3119f639d29d25e4f82ab108b73b28d2e95 100644
--- a/src/.docker_modules/deeptools/3.1.1/Dockerfile
+++ b/src/.docker_modules/deeptools/3.1.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:stretch
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/deeptools/3.1.1/docker_init.sh b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
index a367cac40bcf40270e90755150c541c109ee5ddf..c67c651a91b51532328fbe2464bda6b3982a13b0 100755
--- a/src/.docker_modules/deeptools/3.1.1/docker_init.sh
+++ b/src/.docker_modules/deeptools/3.1.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/deeptools:3.1.1
# docker build src/.docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
# docker push lbmc/deeptools:3.1.1
diff --git a/src/.docker_modules/deeptools/3.5.0/Dockerfile b/src/.docker_modules/deeptools/3.5.0/Dockerfile
index 4680f9494d6c3fca32b27b49f9ee85838f6bb161..577aee240d36f1e81183901137296e189c2a0b0d 100644
--- a/src/.docker_modules/deeptools/3.5.0/Dockerfile
+++ b/src/.docker_modules/deeptools/3.5.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/deeptools/3.5.0/docker_init.sh b/src/.docker_modules/deeptools/3.5.0/docker_init.sh
index d31641fd0a0298df31d1b95cf42c1369c7a11a77..2a295c3800ec0d5790d6eed724aa81d99cf41bf2 100755
--- a/src/.docker_modules/deeptools/3.5.0/docker_init.sh
+++ b/src/.docker_modules/deeptools/3.5.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/deeptools:3.5.0
# docker build src/.docker_modules/deeptools/3.5.0 -t 'lbmc/deeptools:3.5.0'
# docker push lbmc/deeptools:3.5.0
diff --git a/src/.docker_modules/deeptools/3.5.1/Dockerfile b/src/.docker_modules/deeptools/3.5.1/Dockerfile
index 389e85418fe5edda166a1cc976f83d04601c8113..4e1da04dd35e1e8fbc0bf694c247471c314d639b 100644
--- a/src/.docker_modules/deeptools/3.5.1/Dockerfile
+++ b/src/.docker_modules/deeptools/3.5.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.8-slim
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/deeptools/3.5.1/docker_init.sh b/src/.docker_modules/deeptools/3.5.1/docker_init.sh
index 304e988817c7ed38b52806f41c4f2bd333083f71..468152a4d87e13a335296061dc04ae2ac0a82e7d 100755
--- a/src/.docker_modules/deeptools/3.5.1/docker_init.sh
+++ b/src/.docker_modules/deeptools/3.5.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/deeptools:3.5.1
# docker build src/.docker_modules/deeptools/3.5.1 -t 'lbmc/deeptools:3.5.1'
# docker push lbmc/deeptools:3.5.1
diff --git a/src/.docker_modules/docker_push.sh b/src/.docker_modules/docker_push.sh
index 32e0abc1fac52ceb410b03200b80eea96e9b181a..022b3e4d8d907335c645abcb60094c84e143b7b5 100755
--- a/src/.docker_modules/docker_push.sh
+++ b/src/.docker_modules/docker_push.sh
@@ -1,2 +1,7 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
fd "Dockerfile" src/.docker_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'
diff --git a/src/.docker_modules/docker_update.sh b/src/.docker_modules/docker_update.sh
index 39a729bf3b000647df396663343ac7ef64c30f63..20f34b85663cc6463568b5b83d2142b94cc919d5 100644
--- a/src/.docker_modules/docker_update.sh
+++ b/src/.docker_modules/docker_update.sh
@@ -1,2 +1,7 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
fd "Dockerfile" src/.docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker tag "$0" lbmc/" $0)}'
diff --git a/src/.docker_modules/emase-zero/0.3.1/Dockerfile b/src/.docker_modules/emase-zero/0.3.1/Dockerfile
index ac82286db088ea6363fef626d164abe43831f6c4..60bafdd0e5a6462f03abca2cb02beec80d61f9dd 100644
--- a/src/.docker_modules/emase-zero/0.3.1/Dockerfile
+++ b/src/.docker_modules/emase-zero/0.3.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:buster as build
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/emase-zero/0.3.1/docker_init.sh b/src/.docker_modules/emase-zero/0.3.1/docker_init.sh
index 3c92928521995235d49f93fa08579fa0062edc0c..58cd177dd122efecef57a68630b9539c6c0089ca 100755
--- a/src/.docker_modules/emase-zero/0.3.1/docker_init.sh
+++ b/src/.docker_modules/emase-zero/0.3.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/emase-zero:0.3.1
# docker build src/.docker_modules/emase-zero/0.3.1 -t 'lbmc/emase-zero:0.3.1'
# docker push lbmc/emase-zero:0.3.1
diff --git a/src/.docker_modules/emase/0.10.16/Dockerfile b/src/.docker_modules/emase/0.10.16/Dockerfile
index 187d2fb699addc5cf659414fb136439569ceefde..094e0cfd8ecf7b82f975ab9a2c72395712d85c72 100644
--- a/src/.docker_modules/emase/0.10.16/Dockerfile
+++ b/src/.docker_modules/emase/0.10.16/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM conda/miniconda2
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/emase/0.10.16/docker_init.sh b/src/.docker_modules/emase/0.10.16/docker_init.sh
index 9fae4ac78667557b35fada3bc51088fde2d16b9e..83f34512d5d59c61752f8d0853338b6f1adf2856 100755
--- a/src/.docker_modules/emase/0.10.16/docker_init.sh
+++ b/src/.docker_modules/emase/0.10.16/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/emase:0.10.16
# docker build src/.docker_modules/emase/0.10.16 -t 'lbmc/emase:0.10.16'
# docker push lbmc/emase:0.10.16
diff --git a/src/.docker_modules/fastp/0.19.7/Dockerfile b/src/.docker_modules/fastp/0.19.7/Dockerfile
index 234995a7b43807c45e673f6fc64677123cdfd67f..c2b2af84c8e49bfdc813897a4d72b312146de4cc 100644
--- a/src/.docker_modules/fastp/0.19.7/Dockerfile
+++ b/src/.docker_modules/fastp/0.19.7/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/fastp/0.19.7/docker_init.sh b/src/.docker_modules/fastp/0.19.7/docker_init.sh
index 310e5aef0e5e01c20200da089b4fe614aeeac103..b9a5c2f105765a8df5cde8204c809749e935d656 100755
--- a/src/.docker_modules/fastp/0.19.7/docker_init.sh
+++ b/src/.docker_modules/fastp/0.19.7/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/fastp:0.19.7
# docker build src/.docker_modules/fastp/0.19.7 -t 'lbmc/fastp:0.19.7'
# docker push lbmc/fastp:0.19.7
diff --git a/src/.docker_modules/fastp/0.20.1/Dockerfile b/src/.docker_modules/fastp/0.20.1/Dockerfile
index 0461d5ea260b3e894af982a27d1dc8d3b2860c16..abf1becbffdf26c0f6c02b895dbf8dfff1c82d72 100644
--- a/src/.docker_modules/fastp/0.20.1/Dockerfile
+++ b/src/.docker_modules/fastp/0.20.1/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/fastp:0.20.1--h8b12597_0
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/fastp/0.20.1/docker_init.sh b/src/.docker_modules/fastp/0.20.1/docker_init.sh
index 7310a935194e3a15ec32ed784098fc4c06b4fb31..b88ef6cfbb2d29538f8c368d0697fdb0253139dd 100755
--- a/src/.docker_modules/fastp/0.20.1/docker_init.sh
+++ b/src/.docker_modules/fastp/0.20.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/fastp:0.20.1
# docker build src/.docker_modules/fastp/0.20.1 -t 'lbmc/fastp:0.20.1'
# docker push lbmc/fastp:0.20.1
diff --git a/src/.docker_modules/fastp/0.23.2/Dockerfile b/src/.docker_modules/fastp/0.23.2/Dockerfile
index 2ea707ca6850b3dd8cb0d23bc54d517d4253b1a5..cc8b49ad3ecf13eec3267374439e7ca9478d579b 100644
--- a/src/.docker_modules/fastp/0.23.2/Dockerfile
+++ b/src/.docker_modules/fastp/0.23.2/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/fastp:0.23.2--hb7a2d85_2
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/fastp/0.23.2/docker_init.sh b/src/.docker_modules/fastp/0.23.2/docker_init.sh
index b010e7d21016e8819b9cf796652a57f4506de415..d7e9b2512ad668ea411f2d30eba683c939f7a221 100755
--- a/src/.docker_modules/fastp/0.23.2/docker_init.sh
+++ b/src/.docker_modules/fastp/0.23.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/fastp:0.23.2
# docker build src/.docker_modules/fastp/0.23.2 -t 'lbmc/fastp:0.23.2'
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastp:0.23.2" --push src/.docker_modules/fastp/0.23.2
diff --git a/src/.docker_modules/fastqc/0.11.5/Dockerfile b/src/.docker_modules/fastqc/0.11.5/Dockerfile
index 999edf6a3bb5ad548289a0de1740899802ed335d..6fae2451dd2ff7c48a52d5e9ab71464b7a981323 100644
--- a/src/.docker_modules/fastqc/0.11.5/Dockerfile
+++ b/src/.docker_modules/fastqc/0.11.5/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/fastqc/0.11.5/docker_init.sh b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
index 502bbd62228163b18a2d1369d201ae9ac1c8f47a..9807b9f74e37b01fa9937cc0c651f2d3bb561d01 100755
--- a/src/.docker_modules/fastqc/0.11.5/docker_init.sh
+++ b/src/.docker_modules/fastqc/0.11.5/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/fastqc:0.11.5
# docker build src/.docker_modules/fastqc/0.11.5 -t 'lbmc/fastqc:0.11.5'
# docker push lbmc/fastqc:0.11.5
diff --git a/src/.docker_modules/file_handle/0.1.1/Dockerfile b/src/.docker_modules/file_handle/0.1.1/Dockerfile
index 0557983d5d16c686c577b5eee0ee1308086760fb..c9f0902d732f2e624805badc0a10e76950cbe889 100644
--- a/src/.docker_modules/file_handle/0.1.1/Dockerfile
+++ b/src/.docker_modules/file_handle/0.1.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/file_handle/0.1.1/docker_init.sh b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
index 21c51ea0d52e2eb4863acc82760492de1f47d8c8..c0b299e2742776c6c63622b58dba7b7e7c1e5c10 100755
--- a/src/.docker_modules/file_handle/0.1.1/docker_init.sh
+++ b/src/.docker_modules/file_handle/0.1.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/file_handle:0.1.1
# docker build src/.docker_modules/file_handle/0.1.1 -t 'lbmc/file_handle:0.1.1'
# docker push lbmc/file_handle:0.1.1
diff --git a/src/.docker_modules/flexi_splitter/1.0.2/Dockerfile b/src/.docker_modules/flexi_splitter/1.0.2/Dockerfile
index 49f5f7091902703740fbaac084bdebfa1e596fb9..703150f25cf2f56b9de6ebe1c22edfbdf4fe22fd 100644
--- a/src/.docker_modules/flexi_splitter/1.0.2/Dockerfile
+++ b/src/.docker_modules/flexi_splitter/1.0.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/flexi_splitter/1.0.2/docker_init.sh b/src/.docker_modules/flexi_splitter/1.0.2/docker_init.sh
index 7f7c0e77699f32a95df6e452abe2fa658df605c8..0948ba2fa0b2a8850dda9a1f89d4e9e25f9862a7 100755
--- a/src/.docker_modules/flexi_splitter/1.0.2/docker_init.sh
+++ b/src/.docker_modules/flexi_splitter/1.0.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/flexi_splitter:1.0.2
# docker build src/.docker_modules/flexi_splitter/1.0.2 -t 'lbmc/flexi_splitter:1.0.2'
# docker push lbmc/flexi_splitter:1.0.2
diff --git a/src/.docker_modules/freebayes/1.3.2/Dockerfile b/src/.docker_modules/freebayes/1.3.2/Dockerfile
index f696522d1663186e96949ff9a28f79847f048a77..9e103c0728830d51ce4375f02cada1f5de594a1a 100644
--- a/src/.docker_modules/freebayes/1.3.2/Dockerfile
+++ b/src/.docker_modules/freebayes/1.3.2/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/freebayes:1.3.2--py36h89e4507_1
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/freebayes/1.3.2/docker_init.sh b/src/.docker_modules/freebayes/1.3.2/docker_init.sh
index 2e754d0d92af4b7b43902b023ab6ff9d9cc6d510..5d0b440e93a285e98e7079e8fe716582d996e1ee 100755
--- a/src/.docker_modules/freebayes/1.3.2/docker_init.sh
+++ b/src/.docker_modules/freebayes/1.3.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/freebayes:1.3.2
# docker build src/.docker_modules/freebayes/1.3.2/ -t 'lbmc/freebayes:1.3.2'
# docker push lbmc/freebayes:1.3.2
diff --git a/src/.docker_modules/g2gtools/0.2.7/Dockerfile b/src/.docker_modules/g2gtools/0.2.7/Dockerfile
index 6268b9a83d5fbd548e94384a92eeb548d5bc46a2..cfe183d02150041a748e7238c1da6af553ff2368 100644
--- a/src/.docker_modules/g2gtools/0.2.7/Dockerfile
+++ b/src/.docker_modules/g2gtools/0.2.7/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM jcrist/alpine-conda:4.6.8
RUN /opt/conda/bin/conda config --add channels r \
diff --git a/src/.docker_modules/g2gtools/0.2.7/docker_init.sh b/src/.docker_modules/g2gtools/0.2.7/docker_init.sh
index 633690bc685f11ba9a4431ba1903bfc6db654cdb..daad13b4a7ab1aac6037bd36a053bfa26731d44e 100755
--- a/src/.docker_modules/g2gtools/0.2.7/docker_init.sh
+++ b/src/.docker_modules/g2gtools/0.2.7/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/g2gtools:0.2.7
# docker build src/.docker_modules/g2gtools/0.2.7 -t 'lbmc/g2gtools:0.2.7'
# docker push lbmc/g2gtools:0.2.7
diff --git a/src/.docker_modules/g2gtools/0.2.8/Dockerfile b/src/.docker_modules/g2gtools/0.2.8/Dockerfile
index 2163f345c06c5478ca72fe8890cece852f0e78a6..499aa630742aded2679e765c30679e2a2db77826 100644
--- a/src/.docker_modules/g2gtools/0.2.8/Dockerfile
+++ b/src/.docker_modules/g2gtools/0.2.8/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/g2gtools/0.2.8/docker_init.sh b/src/.docker_modules/g2gtools/0.2.8/docker_init.sh
index d09df0f7759d4e9f69f3d1fdbca5b1c538a3fdfd..8133dcfaa9137dbfc9cfde2c6abb7c200b0417ae 100755
--- a/src/.docker_modules/g2gtools/0.2.8/docker_init.sh
+++ b/src/.docker_modules/g2gtools/0.2.8/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/g2gtools:0.2.8
# docker build src/.docker_modules/g2gtools/0.2.8 -t 'lbmc/g2gtools:0.2.8'
# docker push lbmc/g2gtools:0.2.8
diff --git a/src/.docker_modules/gatk/3.8.0/Dockerfile b/src/.docker_modules/gatk/3.8.0/Dockerfile
index af8e30448ea39b16a558d7d4bd8f1fb7ce4b9b2d..c8f7819a4d128a71a9f2cd5656fbf959daf54d6e 100644
--- a/src/.docker_modules/gatk/3.8.0/Dockerfile
+++ b/src/.docker_modules/gatk/3.8.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM broadinstitute/gatk3:3.8-0
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/gatk/3.8.0/docker_init.sh b/src/.docker_modules/gatk/3.8.0/docker_init.sh
index 6378db27d03f6d39311c6478dc3efec975915f75..cb3aebe30c2e9412d8bdf1233a8369c8183bb75c 100755
--- a/src/.docker_modules/gatk/3.8.0/docker_init.sh
+++ b/src/.docker_modules/gatk/3.8.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/gatk:3.8.0
# docker build src/.docker_modules/gatk/3.8.0 -t 'lbmc/gatk:3.8.0'
# docker push lbmc/gatk:3.8.0
diff --git a/src/.docker_modules/gatk/4.0.8.1/Dockerfile b/src/.docker_modules/gatk/4.0.8.1/Dockerfile
index aceded338897254a31dca826413b63cffd933532..c9866de547a1f468231d9986b68ed9ec12d3d67f 100644
--- a/src/.docker_modules/gatk/4.0.8.1/Dockerfile
+++ b/src/.docker_modules/gatk/4.0.8.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM broadinstitute/gatk:4.0.8.1
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/gatk/4.0.8.1/docker_init.sh b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
index 38d06e39cc7030efb6e01a4fcec9d82619556e05..e45d644f071de018f0ac5c88ba71987f9fe8f5f9 100755
--- a/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
+++ b/src/.docker_modules/gatk/4.0.8.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/gatk:4.0.8.1
# docker build src/.docker_modules/gatk/4.0.8.1 -t 'lbmc/gatk:4.0.8.1'
# docker push lbmc/gatk:4.0.8.1
diff --git a/src/.docker_modules/gffread/0.11.8/Dockerfile b/src/.docker_modules/gffread/0.11.8/Dockerfile
index cbb5f60b09e834d05a50d9b4e2d4975577700673..5120e8961dcc7db4612392baf3d0237d8a77051c 100644
--- a/src/.docker_modules/gffread/0.11.8/Dockerfile
+++ b/src/.docker_modules/gffread/0.11.8/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.12
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/gffread/0.11.8/docker_init.sh b/src/.docker_modules/gffread/0.11.8/docker_init.sh
index e03cbd883bfa8bcf130e45c0f07ceabd7895bb90..0248a242d76ecf21423b38aee569a3a76ad7248e 100755
--- a/src/.docker_modules/gffread/0.11.8/docker_init.sh
+++ b/src/.docker_modules/gffread/0.11.8/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/gffread:0.11.8
# docker build src/.docker_modules/gffread/0.11.8 -t 'lbmc/gffread:0.11.8'
# docker push lbmc/gffread:0.11.8
diff --git a/src/.docker_modules/gffread/0.12.2/Dockerfile b/src/.docker_modules/gffread/0.12.2/Dockerfile
index a60a75facd1d5a641231b946181a12ca9a6172c8..b3e416e039b90052b5a0ab9fcceef7ca9f89f197 100644
--- a/src/.docker_modules/gffread/0.12.2/Dockerfile
+++ b/src/.docker_modules/gffread/0.12.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.12
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/gffread/0.12.2/docker_init.sh b/src/.docker_modules/gffread/0.12.2/docker_init.sh
index 174089499432aa9e38c842b8f04df249bab63059..fc2686f6cebd5dc773aa81f8a02bcddae82a71ec 100755
--- a/src/.docker_modules/gffread/0.12.2/docker_init.sh
+++ b/src/.docker_modules/gffread/0.12.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/gffread:0.12.2
# docker build src/.docker_modules/gffread/0.12.2 -t 'lbmc/gffread:0.12.2'
# docker push lbmc/gffread:0.12.2
diff --git a/src/.docker_modules/guppy-cpu/5.0.11/Dockerfile b/src/.docker_modules/guppy-cpu/5.0.11/Dockerfile
index b3ad241370a4786dd5c3ad6de439bdd9e139b712..bda8da63ded93ba734b7af98bc22591806206952 100644
--- a/src/.docker_modules/guppy-cpu/5.0.11/Dockerfile
+++ b/src/.docker_modules/guppy-cpu/5.0.11/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
#Set the base image to Ubuntu 18.04
FROM ubuntu:18.04
diff --git a/src/.docker_modules/guppy-cpu/5.0.11/docker_init.sh b/src/.docker_modules/guppy-cpu/5.0.11/docker_init.sh
index b9968dc3a02f1b0d2a1dbbd7900e1ada8a2e752c..a34b086ac191821960b44a058637e20d3f7662c0 100755
--- a/src/.docker_modules/guppy-cpu/5.0.11/docker_init.sh
+++ b/src/.docker_modules/guppy-cpu/5.0.11/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/guppy-cpu:5.0.11
docker build src/.docker_modules/guppy-cpu/5.0.11 -t 'lbmc/guppy-cpu:5.0.11'
docker push lbmc/guppy-cpu:5.0.11
diff --git a/src/.docker_modules/guppy-cpu/6.0.1/Dockerfile b/src/.docker_modules/guppy-cpu/6.0.1/Dockerfile
index 7fd18203ce04686bc0cbd9fd6235843fe1933c5e..d00918ef029c8ddbcf9e2a85d233271bffc6ec94 100644
--- a/src/.docker_modules/guppy-cpu/6.0.1/Dockerfile
+++ b/src/.docker_modules/guppy-cpu/6.0.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
#Set the base image to Ubuntu 18.04
FROM ubuntu:18.04
diff --git a/src/.docker_modules/guppy-cpu/6.0.1/docker_init.sh b/src/.docker_modules/guppy-cpu/6.0.1/docker_init.sh
index e9cadfff4f8fb6636e09b6d877c5a779f625d24c..043d721fa72b8db5712954521616fd1ba18106fd 100755
--- a/src/.docker_modules/guppy-cpu/6.0.1/docker_init.sh
+++ b/src/.docker_modules/guppy-cpu/6.0.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/guppy-cpu:6.0.1
docker build src/.docker_modules/guppy-cpu/6.0.1 -t 'lbmc/guppy-cpu:6.0.1'
docker push lbmc/guppy-cpu:6.0.1
diff --git a/src/.docker_modules/hicstuff/3.1.3/Dockerfile b/src/.docker_modules/hicstuff/3.1.3/Dockerfile
index 678d0ae40697e3a21083a863f7727722ec184781..da199c922faf37183367aaf80524f7c6107c6634 100644
--- a/src/.docker_modules/hicstuff/3.1.3/Dockerfile
+++ b/src/.docker_modules/hicstuff/3.1.3/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM conda/miniconda3
LABEL Name=hicstuff Version=3.1.3
diff --git a/src/.docker_modules/hicstuff/3.1.3/docker_init.sh b/src/.docker_modules/hicstuff/3.1.3/docker_init.sh
index 009e3fa6a7a350123bc634414a4219b1362d145c..1240b213b99a2c0d3a4fdf89b0c9e3df29fd8b4e 100755
--- a/src/.docker_modules/hicstuff/3.1.3/docker_init.sh
+++ b/src/.docker_modules/hicstuff/3.1.3/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/hicstuff:3.1.3
docker build src/.docker_modules/hicstuff/3.1.3/ -t 'lbmc/hicstuff:3.1.3'
docker push lbmc/hicstuff:3.1.3
diff --git a/src/.docker_modules/hisat2/2.0.0/Dockerfile b/src/.docker_modules/hisat2/2.0.0/Dockerfile
index 6da58508779ea3adfa22c26f672040e8f588b85c..9528172b3595c6d96813dcb5ab939532041dc6b6 100644
--- a/src/.docker_modules/hisat2/2.0.0/Dockerfile
+++ b/src/.docker_modules/hisat2/2.0.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM lbmc/samtools:1.7
MAINTAINER Nicolas Fontrodona
diff --git a/src/.docker_modules/hisat2/2.0.0/docker_init.sh b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
index a09fc9726e4cb19ffb9f80a29a8b22289230e6a2..50336c4da49b044a9c0c15909a5d9cea9a6b30db 100755
--- a/src/.docker_modules/hisat2/2.0.0/docker_init.sh
+++ b/src/.docker_modules/hisat2/2.0.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/hisat2:2.0.0
# docker build src/.docker_modules/hisat2/2.0.0 -t 'lbmc/hisat2:2.0.0'
# docker push lbmc/hisat2:2.0.0
diff --git a/src/.docker_modules/hisat2/2.1.0/Dockerfile b/src/.docker_modules/hisat2/2.1.0/Dockerfile
index 0fc7dacd5984006ac3d0dfebe00dfc42ed050cbd..9cfcb316c4a99a0d25b5f7da1b3eb84173236507 100644
--- a/src/.docker_modules/hisat2/2.1.0/Dockerfile
+++ b/src/.docker_modules/hisat2/2.1.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM lbmc/samtools:1.7
MAINTAINER Nicolas Fontrodona
diff --git a/src/.docker_modules/hisat2/2.1.0/docker_init.sh b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
index 4d541d32ffda61bc7c5c159051a2da3d9b8a54da..b8a6aa5a853113c04d090b5a261454c64743ecdb 100755
--- a/src/.docker_modules/hisat2/2.1.0/docker_init.sh
+++ b/src/.docker_modules/hisat2/2.1.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/hisat2:2.1.0
# docker build src/.docker_modules/hisat2/2.1.0 -t 'lbmc/hisat2:2.1.0'
# docker push lbmc/hisat2:2.1.0
diff --git a/src/.docker_modules/hisat2/2.2.1/Dockerfile b/src/.docker_modules/hisat2/2.2.1/Dockerfile
index 952249c702be595d6485483df7c500affef8a0e6..fc1e746c2b497758b2e028928950c79af74d7acf 100644
--- a/src/.docker_modules/hisat2/2.2.1/Dockerfile
+++ b/src/.docker_modules/hisat2/2.2.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM lbmc/samtools:1.14 as build
ENV HISAT2_VERSION=2.2.1
diff --git a/src/.docker_modules/hisat2/2.2.1/docker_init.sh b/src/.docker_modules/hisat2/2.2.1/docker_init.sh
index adeffb7ec84165125b727bb3fe8a80d8b1f5a3da..238e240ce77052371ea7c8f089870ad4bc790e5d 100755
--- a/src/.docker_modules/hisat2/2.2.1/docker_init.sh
+++ b/src/.docker_modules/hisat2/2.2.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/hisat2:2.2.1
docker build src/.docker_modules/hisat2/2.2.1 -t 'lbmc/hisat2:2.2.1'
docker push lbmc/hisat2:2.2.1
diff --git a/src/.docker_modules/htseq/0.11.2/Dockerfile b/src/.docker_modules/htseq/0.11.2/Dockerfile
index 821d7760af2350605617aea694a92ff2470a9cb7..64071e10c34330c75679257d6ea371f732cbefe6 100644
--- a/src/.docker_modules/htseq/0.11.2/Dockerfile
+++ b/src/.docker_modules/htseq/0.11.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/htseq/0.11.2/docker_init.sh b/src/.docker_modules/htseq/0.11.2/docker_init.sh
index 9e2c73ea967838353653327b57efc23f464a75cc..a4e77f8ae9aa838feee6b64e68019368c73bea30 100644
--- a/src/.docker_modules/htseq/0.11.2/docker_init.sh
+++ b/src/.docker_modules/htseq/0.11.2/docker_init.sh
@@ -1,2 +1,7 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
# docker build src/docker_modules/HTSeq/0.11.2 -t 'htseq:0.11.2'
diff --git a/src/.docker_modules/htseq/0.13.5/Dockerfile b/src/.docker_modules/htseq/0.13.5/Dockerfile
index 68347cf4a63723c11b3a7e4d01817c6ef8d18f79..745e7686d35bb0b09df4369022c268d2840f293a 100644
--- a/src/.docker_modules/htseq/0.13.5/Dockerfile
+++ b/src/.docker_modules/htseq/0.13.5/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/htseq:0.13.5--py39h70b41aa_1
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/htseq/0.13.5/docker_init.sh b/src/.docker_modules/htseq/0.13.5/docker_init.sh
index ca03fe9af2bc8f9f2bb9d70efc02a0c01e40cfde..e9e79ba3b282f90568b2a5eb55a387f68fe4e15b 100755
--- a/src/.docker_modules/htseq/0.13.5/docker_init.sh
+++ b/src/.docker_modules/htseq/0.13.5/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/htseq:0.13.5
docker build src/.docker_modules/htseq/0.13.5 -t 'lbmc/htseq:0.13.5'
docker push lbmc/htseq:0.13.5
diff --git a/src/.docker_modules/htseq/0.8.0/Dockerfile b/src/.docker_modules/htseq/0.8.0/Dockerfile
index 492d91a697b945a3acd3aa3bd0ebb09590fb3de5..6f118d1a0488fe34f4486927560d9d35276b2424 100644
--- a/src/.docker_modules/htseq/0.8.0/Dockerfile
+++ b/src/.docker_modules/htseq/0.8.0/Dockerfile
@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/htseq/0.8.0/docker_init.sh b/src/.docker_modules/htseq/0.8.0/docker_init.sh
index 7535289438cdc687a1e5739deca28b14b7426c9f..41f668e33191ed154383b18315090d9eccfd5203 100755
--- a/src/.docker_modules/htseq/0.8.0/docker_init.sh
+++ b/src/.docker_modules/htseq/0.8.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/htseq:0.8.0
# docker build src/.docker_modules/htseq/0.8.0 -t 'lbmc/htseq:0.8.0'
# docker push lbmc/htseq:0.8.0
diff --git a/src/.docker_modules/htseq/1.99.2/Dockerfile b/src/.docker_modules/htseq/1.99.2/Dockerfile
index eceb5c8175f6519a3d5210231c1fa0eeb856431f..801483ef8e27eeda7a544f6ce3b20cdc90c04857 100644
--- a/src/.docker_modules/htseq/1.99.2/Dockerfile
+++ b/src/.docker_modules/htseq/1.99.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:20.04
RUN apt-get update \
diff --git a/src/.docker_modules/htseq/1.99.2/docker_init.sh b/src/.docker_modules/htseq/1.99.2/docker_init.sh
index a0aa647971875e01cfd0a2e9949aa9cadaf6cec2..6c7319f0a70289e2f15c01d6c769a877ed812cf2 100755
--- a/src/.docker_modules/htseq/1.99.2/docker_init.sh
+++ b/src/.docker_modules/htseq/1.99.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/htseq:1.99.2
docker build src/.docker_modules/htseq/1.99.2 -t 'lbmc/htseq:1.99.2'
docker push lbmc/htseq:1.99.2
diff --git a/src/.docker_modules/kallisto/0.43.1/Dockerfile b/src/.docker_modules/kallisto/0.43.1/Dockerfile
index 68a731a7fad98ed9c423909797d259baf2ea66eb..6803f874081f29eaa0c8e98cf6b108a44950b90d 100644
--- a/src/.docker_modules/kallisto/0.43.1/Dockerfile
+++ b/src/.docker_modules/kallisto/0.43.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/kallisto/0.43.1/docker_init.sh b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
index b4043c7102a70c8e8a4eab4f11e9a4caa9c285e0..f488c75426ec0c5737b5d540ffe5243cedb21771 100755
--- a/src/.docker_modules/kallisto/0.43.1/docker_init.sh
+++ b/src/.docker_modules/kallisto/0.43.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/kallisto:0.43.1
# docker build src/.docker_modules/kallisto/0.43.1 -t 'lbmc/kallisto:0.43.1'
# docker push lbmc/kallisto:0.43.1
diff --git a/src/.docker_modules/kallisto/0.44.0/Dockerfile b/src/.docker_modules/kallisto/0.44.0/Dockerfile
index 9c4dd013e34bf76c4dcd408622eebccbe3e52396..13f5c12e4224a138c95a1b06e5efb3ccd83f1051 100644
--- a/src/.docker_modules/kallisto/0.44.0/Dockerfile
+++ b/src/.docker_modules/kallisto/0.44.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/kallisto/0.44.0/docker_init.sh b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
index e3670b68417db2189b04ac00af3139400b4b3fd3..a74feb9a05c86553e30bc07b34827e2c61412ed0 100755
--- a/src/.docker_modules/kallisto/0.44.0/docker_init.sh
+++ b/src/.docker_modules/kallisto/0.44.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/kallisto:0.44.0
# docker build src/.docker_modules/kallisto/0.44.0 -t 'lbmc/kallisto:0.44.0'
# docker push lbmc/kallisto:0.44.0
diff --git a/src/.docker_modules/kallistobustools/0.24.4/Dockerfile b/src/.docker_modules/kallistobustools/0.24.4/Dockerfile
index b3bb53556f54e2e47510dd89d79e273ea2f3723f..c41e864269d10e1f497d82640060810e688e68f5 100644
--- a/src/.docker_modules/kallistobustools/0.24.4/Dockerfile
+++ b/src/.docker_modules/kallistobustools/0.24.4/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.7
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh b/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh
index bb0edc976b6d56be250ab54b266c24a9672bccf4..82c45b81ece208bbcebaa6e7a3d109363f03ccdb 100755
--- a/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh
+++ b/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/kallistobustools:0.24.4
# docker build src/.docker_modules/kallistobustools/0.24.4 -t 'lbmc/kallistobustools:0.24.4'
# docker push lbmc/kallistobustools:0.24.4
diff --git a/src/.docker_modules/kallistobustools/0.39.3/Dockerfile b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
index 1649aeedd22d978ce3591e3b2c227abf1e3aa2be..a4ae734d02d3706b2d8ed38b16f1c68f9c1c3a26 100644
--- a/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
+++ b/src/.docker_modules/kallistobustools/0.39.3/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.8-alpine
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh b/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
index 9ba2835a5f2287d334900e7b4ce17e89cde95049..a815d9b831630d36e448c07d8acbde5d56ee364e 100755
--- a/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
+++ b/src/.docker_modules/kallistobustools/0.39.3/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/kallistobustools:0.39.3
# docker build src/.docker_modules/kallistobustools/0.39.3 -t 'lbmc/kallistobustools:0.39.3'
# docker push lbmc/kallistobustools:0.39.3
diff --git a/src/.docker_modules/kb/0.26.0/Dockerfile b/src/.docker_modules/kb/0.26.0/Dockerfile
index 374646355b3f3f3895e8450c70d49eec1688c280..7821320a78c3c5551e1369dcb436e98bb2f2e5c8 100644
--- a/src/.docker_modules/kb/0.26.0/Dockerfile
+++ b/src/.docker_modules/kb/0.26.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
ENV KB_VERSION="0.26.0"
diff --git a/src/.docker_modules/kb/0.26.0/docker_init.sh b/src/.docker_modules/kb/0.26.0/docker_init.sh
index 4531914965e15aa627ba65938d1cbb0ef673483a..be1c46310762b9350bc23f5b2fd5fd41bf4c848c 100755
--- a/src/.docker_modules/kb/0.26.0/docker_init.sh
+++ b/src/.docker_modules/kb/0.26.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/kb:0.26.0
# docker build src/.docker_modules/kb/0.26.0 -t 'lbmc/kb:0.26.0'
# docker push lbmc/kb:0.26.0
diff --git a/src/.docker_modules/kb/0.26.0/fix_t2g.py b/src/.docker_modules/kb/0.26.0/fix_t2g.py
index a6b4619b5a17ad3fd4351918eb77c13b8c106f94..ea98e7a237337cc3e342c020095ffc6e86e963f3 100644
--- a/src/.docker_modules/kb/0.26.0/fix_t2g.py
+++ b/src/.docker_modules/kb/0.26.0/fix_t2g.py
@@ -1,4 +1,9 @@
#!/usr/local/bin/python
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
import os
import re
import gzip
diff --git a/src/.docker_modules/kb/0.26.0/t2g.py b/src/.docker_modules/kb/0.26.0/t2g.py
index b99e74e6c2c3d9574ce54008bc58143c14b229a5..cf9ca7c678bf6c498c65f2b6a8dbe8d675261f68 100755
--- a/src/.docker_modules/kb/0.26.0/t2g.py
+++ b/src/.docker_modules/kb/0.26.0/t2g.py
@@ -1,4 +1,9 @@
#!/usr/local/bin/python
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
import os
import re
import gzip
diff --git a/src/.docker_modules/kb/0.26.3/Dockerfile b/src/.docker_modules/kb/0.26.3/Dockerfile
index 5cd35dfae7d474b25223ebeca80fe6adada91db3..ad9036315bccd66f838305dcd01a7cc8ba7f78e5 100644
--- a/src/.docker_modules/kb/0.26.3/Dockerfile
+++ b/src/.docker_modules/kb/0.26.3/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
ENV KB_VERSION="0.26.3"
diff --git a/src/.docker_modules/kb/0.26.3/docker_init.sh b/src/.docker_modules/kb/0.26.3/docker_init.sh
index 0294274a2518ef8622027bb56b49c4baded4a9d8..e78f050809b09dcd1c3afcd53624e629ab906662 100755
--- a/src/.docker_modules/kb/0.26.3/docker_init.sh
+++ b/src/.docker_modules/kb/0.26.3/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/kb:0.26.3
docker build src/.docker_modules/kb/0.26.3 -t 'lbmc/kb:0.26.3'
docker push lbmc/kb:0.26.3
diff --git a/src/.docker_modules/kb/0.26.3/t2g.py b/src/.docker_modules/kb/0.26.3/t2g.py
index f9f0b45dc89b385c3ed52dc252f8f09eb3bc8c74..6499927f26b52bc5b5108cbc8ffc018b062c71db 100755
--- a/src/.docker_modules/kb/0.26.3/t2g.py
+++ b/src/.docker_modules/kb/0.26.3/t2g.py
@@ -1,4 +1,9 @@
#!/usr/local/bin/python
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
import os
import gffutils
import argparse
diff --git a/src/.docker_modules/last/1060/Dockerfile b/src/.docker_modules/last/1060/Dockerfile
index 4193a11f30d443b870a188bebffc33c56038d336..bad3d5a367ec67c822fd16638fac0ec60d083b6e 100644
--- a/src/.docker_modules/last/1060/Dockerfile
+++ b/src/.docker_modules/last/1060/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/last/1060/docker_init.sh b/src/.docker_modules/last/1060/docker_init.sh
index e5682dfdf46a796352dbfa5068cd5e0e6001adf3..73abd3662c74feaf868c6cfa011b71532edf2002 100755
--- a/src/.docker_modules/last/1060/docker_init.sh
+++ b/src/.docker_modules/last/1060/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/last:1060
# docker build src/.docker_modules/last/1060/ -t 'lbmc/last:1060'
# docker push lbmc/last:1060
diff --git a/src/.docker_modules/liftover/357/Dockerfile b/src/.docker_modules/liftover/357/Dockerfile
index 973a1dc03c9cc8c73209f13f1fecf84906b8be7b..14aef23ceab841899605027cb990c7a7e5c088a9 100644
--- a/src/.docker_modules/liftover/357/Dockerfile
+++ b/src/.docker_modules/liftover/357/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/ucsc-liftover:357--1
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/liftover/357/docker_init.sh b/src/.docker_modules/liftover/357/docker_init.sh
index 1f4da570565e97ea69275452ca68b5fb4004973c..2b3561d824cae4d95229c55c9126cf08668e2f58 100755
--- a/src/.docker_modules/liftover/357/docker_init.sh
+++ b/src/.docker_modules/liftover/357/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/liftover:357
# docker build src/.docker_modules/liftover/357/ -t 'lbmc/liftover:357'
# docker push lbmc/liftover:357
diff --git a/src/.docker_modules/macs2/2.1.2/Dockerfile b/src/.docker_modules/macs2/2.1.2/Dockerfile
index 71979a50044cd8ce9c52f1d413db269088d352dd..bc544b040d6d88543c8926df0f9e2b244efd2dba 100644
--- a/src/.docker_modules/macs2/2.1.2/Dockerfile
+++ b/src/.docker_modules/macs2/2.1.2/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/macs2/2.1.2/docker_init.sh b/src/.docker_modules/macs2/2.1.2/docker_init.sh
index 70f61fcd41109c398c4db60f4fcea2f69b9bbbcb..2958428b4dc0b858ff71938326d493a2089afe62 100755
--- a/src/.docker_modules/macs2/2.1.2/docker_init.sh
+++ b/src/.docker_modules/macs2/2.1.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/macs2:2.1.2
# docker build src/.docker_modules/macs2/2.1.2 -t 'lbmc/macs2:2.1.2'
# docker push lbmc/macs2:2.1.2
diff --git a/src/.docker_modules/macs3/3.0.0a6/Dockerfile b/src/.docker_modules/macs3/3.0.0a6/Dockerfile
index 375b8f631fe40f9e05f94400d15057f303713438..856be5c4d6bc2344d7a2c718c7c1a7f23fd6b47c 100644
--- a/src/.docker_modules/macs3/3.0.0a6/Dockerfile
+++ b/src/.docker_modules/macs3/3.0.0a6/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/macs3/3.0.0a6/docker_init.sh b/src/.docker_modules/macs3/3.0.0a6/docker_init.sh
index ab969f74738ed154e031f85315fa1a79d27e6703..5e0bd5137e593cee4b760a3d88af4ea0a20566fc 100755
--- a/src/.docker_modules/macs3/3.0.0a6/docker_init.sh
+++ b/src/.docker_modules/macs3/3.0.0a6/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/macs3:3.0.0a6
# docker build src/.docker_modules/macs3/3.0.0a6 -t 'lbmc/macs3:3.0.0a6'
# docker push lbmc/macs3:3.0.0a6
diff --git a/src/.docker_modules/minimap2/2.17/Dockerfile b/src/.docker_modules/minimap2/2.17/Dockerfile
index 1f5b05c02b573cc8d7392c53213cc78cbb6abeb5..cfb737705b4307f7929f1273e4055a8c7994db00 100644
--- a/src/.docker_modules/minimap2/2.17/Dockerfile
+++ b/src/.docker_modules/minimap2/2.17/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools
# /usr/local/bin/samtools
# / # ldd /usr/local/bin/samtools
diff --git a/src/.docker_modules/minimap2/2.17/docker_init.sh b/src/.docker_modules/minimap2/2.17/docker_init.sh
index c77f5b7879ced88a2533b81f263b80b771a39043..2496e35d718152c7a5d25a5f0bb4d50e789d7674 100755
--- a/src/.docker_modules/minimap2/2.17/docker_init.sh
+++ b/src/.docker_modules/minimap2/2.17/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/minimap2:2.17
# docker build src/.docker_modules/minimap2/2.17 -t 'lbmc/minimap2:2.17'
# docker push lbmc/minimap2:2.17
diff --git a/src/.docker_modules/minimap2/2.20/Dockerfile b/src/.docker_modules/minimap2/2.20/Dockerfile
index e3f6ab63666ec0a10adafb5ef0d2f9180564dffe..793c0d2817d7823a641590634142f91214b05219 100644
--- a/src/.docker_modules/minimap2/2.20/Dockerfile
+++ b/src/.docker_modules/minimap2/2.20/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools
# /usr/local/bin/samtools
# / # ldd /usr/local/bin/samtools
diff --git a/src/.docker_modules/minimap2/2.20/docker_init.sh b/src/.docker_modules/minimap2/2.20/docker_init.sh
index 113d4cd9392d2e57241413a2359465f5f1683e5f..b1cb27a1299ce6eb3c84bfa5728947cf45257349 100755
--- a/src/.docker_modules/minimap2/2.20/docker_init.sh
+++ b/src/.docker_modules/minimap2/2.20/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/minimap2:2.20
docker build src/.docker_modules/minimap2/2.20 -t 'lbmc/minimap2:2.20'
docker push lbmc/minimap2:2.20
diff --git a/src/.docker_modules/minimap2/2.24/Dockerfile b/src/.docker_modules/minimap2/2.24/Dockerfile
index 01301e7573bb7c7f63155a7d795a4fcea0d605cf..a662ebdce2fc9df1bfd792c574165d4ee247c4dc 100644
--- a/src/.docker_modules/minimap2/2.24/Dockerfile
+++ b/src/.docker_modules/minimap2/2.24/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools
# /usr/local/bin/samtools
# / # ldd /usr/local/bin/samtools
diff --git a/src/.docker_modules/minimap2/2.24/docker_init.sh b/src/.docker_modules/minimap2/2.24/docker_init.sh
index 07958443a901a9d2d6c474eaa13498646023f412..b16243008490ddf996b8317b03f1f9d921349aa0 100755
--- a/src/.docker_modules/minimap2/2.24/docker_init.sh
+++ b/src/.docker_modules/minimap2/2.24/docker_init.sh
@@ -1,5 +1,10 @@
#!/bin/sh
- docker pull lbmc/minimap2:2.24
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/minimap2:2.24
docker build src/.docker_modules/minimap2/2.24 -t 'lbmc/minimap2:2.24'
docker push lbmc/minimap2:2.24
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/minimap2:2.24" --push src/.docker_modules/minimap2/2.24
\ No newline at end of file
diff --git a/src/.docker_modules/multiqc/1.0/Dockerfile b/src/.docker_modules/multiqc/1.0/Dockerfile
index 7acf600c99d9f3500bf015d4b79e3675ac5d7789..48bd41cbc99cb3beed6201a2d1ecd2091c8da15d 100644
--- a/src/.docker_modules/multiqc/1.0/Dockerfile
+++ b/src/.docker_modules/multiqc/1.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:stretch
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/multiqc/1.0/docker_init.sh b/src/.docker_modules/multiqc/1.0/docker_init.sh
index a0098e2fdf2fbe5091543f0a872c47c2669a18d0..7f72c3d585aabbbd4ed67a54e9c8305ec34ebe43 100755
--- a/src/.docker_modules/multiqc/1.0/docker_init.sh
+++ b/src/.docker_modules/multiqc/1.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/multiqc:1.0
# docker build src/.docker_modules/multiqc/1.0 -t 'lbmc/multiqc:1.0'
# docker push lbmc/multiqc:1.0
diff --git a/src/.docker_modules/multiqc/1.11/Dockerfile b/src/.docker_modules/multiqc/1.11/Dockerfile
index cd6e68e662bdd660e3c58f2ad51ff72ec1e7bfa5..fb992d7d60454e57e99494f52b2ce427b9c1c10d 100644
--- a/src/.docker_modules/multiqc/1.11/Dockerfile
+++ b/src/.docker_modules/multiqc/1.11/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/multiqc/1.11/docker_init.sh b/src/.docker_modules/multiqc/1.11/docker_init.sh
index 5831c6eccde183ac2c129757436bba1823bb45c3..07ab664dcd51383a2b074326ff61ec0f730cb0e8 100755
--- a/src/.docker_modules/multiqc/1.11/docker_init.sh
+++ b/src/.docker_modules/multiqc/1.11/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/multiqc:1.11
# docker build src/.docker_modules/multiqc/1.11 -t 'lbmc/multiqc:1.11'
# docker push lbmc/multiqc:1.11
diff --git a/src/.docker_modules/multiqc/1.7/Dockerfile b/src/.docker_modules/multiqc/1.7/Dockerfile
index ea71b1ad8227b9456863b7b00fc5d818db090288..10922494b0b5a706995eb5c6b1647427e10c292a 100644
--- a/src/.docker_modules/multiqc/1.7/Dockerfile
+++ b/src/.docker_modules/multiqc/1.7/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:stretch
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/multiqc/1.7/docker_init.sh b/src/.docker_modules/multiqc/1.7/docker_init.sh
index 375f5a3b9c30070a09098456a93afc46408a5a46..c18631a96a8ed47ccae9294ef224b0ebe89cf24e 100755
--- a/src/.docker_modules/multiqc/1.7/docker_init.sh
+++ b/src/.docker_modules/multiqc/1.7/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/multiqc:1.7
# docker build src/.docker_modules/multiqc/1.7 -t 'lbmc/multiqc:1.7'
# docker push lbmc/multiqc:1.7
diff --git a/src/.docker_modules/multiqc/1.9/Dockerfile b/src/.docker_modules/multiqc/1.9/Dockerfile
index 3e82ccb436f841876ef71c73f4e6a611454bd7f2..fefd2693e7c851e6469ef38896c465a4838f8426 100644
--- a/src/.docker_modules/multiqc/1.9/Dockerfile
+++ b/src/.docker_modules/multiqc/1.9/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:stretch
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/multiqc/1.9/docker_init.sh b/src/.docker_modules/multiqc/1.9/docker_init.sh
index b47d3cde6b23b65ffb2b9ca0062ffcf9541d8700..de1ebe8dd2006548e6f72053d3739a3bb8cd91fb 100755
--- a/src/.docker_modules/multiqc/1.9/docker_init.sh
+++ b/src/.docker_modules/multiqc/1.9/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/multiqc:1.9
# docker build src/.docker_modules/multiqc/1.9 -t 'lbmc/multiqc:1.9'
# docker push lbmc/multiqc:1.9
diff --git a/src/.docker_modules/music/6613c53/Dockerfile b/src/.docker_modules/music/6613c53/Dockerfile
index aa47eb572ca48736457bb0f60b0857bbe6c5d9df..7b310beb490971c1697f67965e5a8bef55a67c38 100644
--- a/src/.docker_modules/music/6613c53/Dockerfile
+++ b/src/.docker_modules/music/6613c53/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.8
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/music/6613c53/docker_init.sh b/src/.docker_modules/music/6613c53/docker_init.sh
index 9ef317a11822b5abc4760053458a4aba700c8a41..6da1fae2d38fae72d4939655163c2b9498cd400c 100755
--- a/src/.docker_modules/music/6613c53/docker_init.sh
+++ b/src/.docker_modules/music/6613c53/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/music:6613c53
# docker build src/.docker_modules/music/6613c53 -t 'lbmc/music:6613c53'
# docker push lbmc/music:6613c53
diff --git a/src/.docker_modules/pandoc/2.11/Dockerfile b/src/.docker_modules/pandoc/2.11/Dockerfile
index f62b84b960032314a2fb43daedd10d6b539a0c91..908ffc3e54d3d6de8fd3e94c2a2846cf309a92e7 100644
--- a/src/.docker_modules/pandoc/2.11/Dockerfile
+++ b/src/.docker_modules/pandoc/2.11/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.13
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/pandoc/2.11/docker_init.sh b/src/.docker_modules/pandoc/2.11/docker_init.sh
index 309f146d22c7784c5e035c649f142104bdb5a714..dd69e1dc8c0a35fc56b40c5217cca81a9dbf36c3 100755
--- a/src/.docker_modules/pandoc/2.11/docker_init.sh
+++ b/src/.docker_modules/pandoc/2.11/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/pandoc:2.11
# docker build src/.docker_modules/pandoc/2.11 -t 'lbmc/pandoc:2.11'
# docker push lbmc/pandoc:2.11
diff --git a/src/.docker_modules/picard/2.18.11/Dockerfile b/src/.docker_modules/picard/2.18.11/Dockerfile
index 6a358e55bf36a4be4842335f47491ec8ac3a4ced..f36f35b6e7de0ece79e79f7aaa27eb1342e4c7c5 100644
--- a/src/.docker_modules/picard/2.18.11/Dockerfile
+++ b/src/.docker_modules/picard/2.18.11/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/picard/2.18.11/PicardCommandLine b/src/.docker_modules/picard/2.18.11/PicardCommandLine
index c8eebf8345906cae9ef2e63409500857de479f09..f71fedc9f2dc97e2237495571483f64b13f00621 100644
--- a/src/.docker_modules/picard/2.18.11/PicardCommandLine
+++ b/src/.docker_modules/picard/2.18.11/PicardCommandLine
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
set -eu
PRG="$(basename -- "$0")"
case "$PRG" in
diff --git a/src/.docker_modules/picard/2.18.11/docker_init.sh b/src/.docker_modules/picard/2.18.11/docker_init.sh
index 6e77b810f498da965b7181d1b243e321281218f9..011e335198e5dd55cf9a2bbfcf3d47aa7553d0d1 100755
--- a/src/.docker_modules/picard/2.18.11/docker_init.sh
+++ b/src/.docker_modules/picard/2.18.11/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/picard:2.18.11
# docker build src/.docker_modules/picard/2.18.11 -t 'lbmc/picard:2.18.11'
# docker push lbmc/picard:2.18.11
diff --git a/src/.docker_modules/pigz/2.4/Dockerfile b/src/.docker_modules/pigz/2.4/Dockerfile
index 75f9e2fcfd9b5394b45fbfa4541861e6e4ab43e1..692e299286c2b4cdc758481e5ddb11b8952cec7d 100644
--- a/src/.docker_modules/pigz/2.4/Dockerfile
+++ b/src/.docker_modules/pigz/2.4/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/pigz/2.4/docker_init.sh b/src/.docker_modules/pigz/2.4/docker_init.sh
index 2925b0b6f692d1ded62fb54a93f304186d212d3c..a45aa3b2c64a4ccb7df078dc1ebc4d26cacd0ccf 100755
--- a/src/.docker_modules/pigz/2.4/docker_init.sh
+++ b/src/.docker_modules/pigz/2.4/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/pigz:2.4
# docker build src/.docker_modules/pigz/2.4 -t 'lbmc/pigz:2.4'
# docker push lbmc/pigz:2.4
diff --git a/src/.docker_modules/porechop/0.2.4/Dockerfile b/src/.docker_modules/porechop/0.2.4/Dockerfile
index c88f9f82160e86570b686682a8a6e332d317ec2c..9df96f1c9c6eb33465b17899cdd072821b23f360 100644
--- a/src/.docker_modules/porechop/0.2.4/Dockerfile
+++ b/src/.docker_modules/porechop/0.2.4/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
###############################################
# Dockerfile to build poretools container image
# Based on Ubuntu 16.04
diff --git a/src/.docker_modules/porechop/0.2.4/docker_init.sh b/src/.docker_modules/porechop/0.2.4/docker_init.sh
index 1950947837fe2b381b8423cf9d2a16e43e1c152a..6eb17bf622a1640b93babf8aba8842dfc069ba0d 100755
--- a/src/.docker_modules/porechop/0.2.4/docker_init.sh
+++ b/src/.docker_modules/porechop/0.2.4/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/porechop:0.2.4
docker build src/.docker_modules/porechop/0.2.4 -t 'lbmc/porechop:0.2.4'
docker push lbmc/porechop:0.2.4
diff --git a/src/.docker_modules/python/3.8/Dockerfile b/src/.docker_modules/python/3.8/Dockerfile
index 20b4edd3aaa75374695afb4ca34c7be889e01933..c4a86e8cdca9626ecf0b03b9e7fc3f7bc00394e3 100644
--- a/src/.docker_modules/python/3.8/Dockerfile
+++ b/src/.docker_modules/python/3.8/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.8.0a3-stretch
MAINTAINER Remi Seraphin
diff --git a/src/.docker_modules/python/3.8/docker_init.sh b/src/.docker_modules/python/3.8/docker_init.sh
index 29a251fcaca93765eaa1d843b8d8486db2342d8f..5e42fd44822a9b957c445d96fc18d47800625b0b 100755
--- a/src/.docker_modules/python/3.8/docker_init.sh
+++ b/src/.docker_modules/python/3.8/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/python:3.8
# docker build src/.docker_modules/python/3.8 -t 'lbmc/python:3.8'
# docker push lbmc/python:3.8
diff --git a/src/.docker_modules/r-base/3.5.3/Dockerfile b/src/.docker_modules/r-base/3.5.3/Dockerfile
index 7c937de7a166d84c0bf75fe4a17fb4b162d61391..f5171b5764b9a9ee05035436d569b52fc13bdecd 100644
--- a/src/.docker_modules/r-base/3.5.3/Dockerfile
+++ b/src/.docker_modules/r-base/3.5.3/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM rocker/r-ver:3.5.3
MAINTAINER Remi Seraphin
diff --git a/src/.docker_modules/r-base/3.5.3/docker_init.sh b/src/.docker_modules/r-base/3.5.3/docker_init.sh
index 7e0a931bc9affe03242282d21acea352f1ba8926..aae415f8d948f365558ae6f421eaf3be885bb6e5 100755
--- a/src/.docker_modules/r-base/3.5.3/docker_init.sh
+++ b/src/.docker_modules/r-base/3.5.3/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/r:3.5.3
# docker build src/.docker_modules/r-base/3.5.3 -t 'lbmc/r:3.5.3'
# docker push lbmc/r:3.5.3
diff --git a/src/.docker_modules/r-base/3.6.2/Dockerfile b/src/.docker_modules/r-base/3.6.2/Dockerfile
index fd4dcf7867019a2ecb73241fd0d6d39c7196fec1..e89cb94a9adba62695adffaff6bb869e7cf68f28 100644
--- a/src/.docker_modules/r-base/3.6.2/Dockerfile
+++ b/src/.docker_modules/r-base/3.6.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.11.5
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/r-base/3.6.2/docker_init.sh b/src/.docker_modules/r-base/3.6.2/docker_init.sh
index 29a3ea6716c078c79437f428a8a70226351e2123..f41a78c846cdf06dabb488dfabd88befab11b3fc 100755
--- a/src/.docker_modules/r-base/3.6.2/docker_init.sh
+++ b/src/.docker_modules/r-base/3.6.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/r-base:3.6.2
# docker build src/.docker_modules/r-base/3.6.2 -t 'lbmc/r-base:3.6.2'
# docker push lbmc/r-base:3.6.2
diff --git a/src/.docker_modules/r-base/4.0.0/Dockerfile b/src/.docker_modules/r-base/4.0.0/Dockerfile
index 6bfa98a516d2cf1ca66d07ffc8749ad1c57240d4..e676024dfe24e0d0b7ffe42d74cbae654283a55a 100644
--- a/src/.docker_modules/r-base/4.0.0/Dockerfile
+++ b/src/.docker_modules/r-base/4.0.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.12.0
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/r-base/4.0.0/docker_init.sh b/src/.docker_modules/r-base/4.0.0/docker_init.sh
index d5010649517234b79e63ad3fc6e32c85b2207f59..521b8a2238f756dd0cb09cd71680442c90002894 100755
--- a/src/.docker_modules/r-base/4.0.0/docker_init.sh
+++ b/src/.docker_modules/r-base/4.0.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/r-base:4.0.0
# docker build src/.docker_modules/r-base/4.0.0 -t 'lbmc/r-base:4.0.0'
# docker push lbmc/r-base:4.0.0
diff --git a/src/.docker_modules/r-base/4.0.2/Dockerfile b/src/.docker_modules/r-base/4.0.2/Dockerfile
index 97e111459c9b685fa6abd6b18fbdf880ffe81bc9..ae37b382a5e340d75b2da7ee654633107f3eac46 100644
--- a/src/.docker_modules/r-base/4.0.2/Dockerfile
+++ b/src/.docker_modules/r-base/4.0.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.12.0
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/r-base/4.0.2/docker_init.sh b/src/.docker_modules/r-base/4.0.2/docker_init.sh
index 7a5e7304c4d77f4210c0ca1c110d122910cddf4a..f59333bc9ac745aa56291cf42cf17a490824e40d 100755
--- a/src/.docker_modules/r-base/4.0.2/docker_init.sh
+++ b/src/.docker_modules/r-base/4.0.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/r-base:4.0.2
# docker build src/.docker_modules/r-base/4.0.2 -t 'lbmc/r-base:4.0.2'
# docker push lbmc/r-base:4.0.2
diff --git a/src/.docker_modules/r-base/4.0.3/Dockerfile b/src/.docker_modules/r-base/4.0.3/Dockerfile
index 58f752ff581aca0270beebd74e4c9abf8d0e7e8a..91e0f14edf8910f33e7455b7d859d37c37d218d4 100644
--- a/src/.docker_modules/r-base/4.0.3/Dockerfile
+++ b/src/.docker_modules/r-base/4.0.3/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.13.1
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/r-base/4.0.3/docker_init.sh b/src/.docker_modules/r-base/4.0.3/docker_init.sh
index 4679de3a4de54dbb7c8ea3c18082e0a666fa1f14..12a8c72827de3279e101cdd85f569ef46ef0150f 100755
--- a/src/.docker_modules/r-base/4.0.3/docker_init.sh
+++ b/src/.docker_modules/r-base/4.0.3/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/r-base:4.0.3
# docker build src/.docker_modules/r-base/4.0.3 -t 'lbmc/r-base:4.0.3'
# docker push lbmc/r-base:4.0.3
diff --git a/src/.docker_modules/r-base/4.1.2/Dockerfile b/src/.docker_modules/r-base/4.1.2/Dockerfile
index 64a822b9d2d8de5b6d1fb55c827c064f24099e1d..db99ebe56316933c7b8f53afcf11df3ea037e0a5 100644
--- a/src/.docker_modules/r-base/4.1.2/Dockerfile
+++ b/src/.docker_modules/r-base/4.1.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.15
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/r-base/4.1.2/docker_init.sh b/src/.docker_modules/r-base/4.1.2/docker_init.sh
index 7d337558caa384b4137f0f28f70a89149b43de45..3d0cd87d6b256bf9270fe286fd8ed5b0a5549564 100755
--- a/src/.docker_modules/r-base/4.1.2/docker_init.sh
+++ b/src/.docker_modules/r-base/4.1.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/r-base:4.1.2
# docker build src/.docker_modules/r-base/4.1.2 -t 'lbmc/r-base:4.1.2'
# docker push lbmc/r-base:4.1.2
diff --git a/src/.docker_modules/rasusa/0.6.0/Dockerfile b/src/.docker_modules/rasusa/0.6.0/Dockerfile
index 00ee62f6ab38676c8e97ae103bd0932498238e45..2a8bea180bbb758d70ab41d8a65b5ed4fc629db1 100644
--- a/src/.docker_modules/rasusa/0.6.0/Dockerfile
+++ b/src/.docker_modules/rasusa/0.6.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/mbhall88/rasusa:0.6.0 AS quay_source
FROM alpine:3.13
diff --git a/src/.docker_modules/rasusa/0.6.0/docker_init.sh b/src/.docker_modules/rasusa/0.6.0/docker_init.sh
index 4f920288e1281d8c05a9fcd7c86aceff9b0c4d4a..c7f69ce9f8311e2737828853b400c25c9b0f7fda 100755
--- a/src/.docker_modules/rasusa/0.6.0/docker_init.sh
+++ b/src/.docker_modules/rasusa/0.6.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/rasusa:0.6.0
# docker build src/.docker_modules/rasusa/0.6.0 -t 'lbmc/rasusa:0.6.0'
# docker push lbmc/rasusa:0.6.0
diff --git a/src/.docker_modules/ribotricer/1.3.2/Dockerfile b/src/.docker_modules/ribotricer/1.3.2/Dockerfile
index 451a68a1fdf14d8e517f6aad5504f516993cfa1f..d341683e17dbc2eb7d60bf0c571752127cab2994 100644
--- a/src/.docker_modules/ribotricer/1.3.2/Dockerfile
+++ b/src/.docker_modules/ribotricer/1.3.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:20.04
MAINTAINER Emmanuel Labaronne
diff --git a/src/.docker_modules/ribotricer/1.3.2/docker_init.sh b/src/.docker_modules/ribotricer/1.3.2/docker_init.sh
index b28b00c5db0df0dba25c789275c99393f6356279..491c61b1002cf1da1af077cdc9e12b0fd8227c03 100644
--- a/src/.docker_modules/ribotricer/1.3.2/docker_init.sh
+++ b/src/.docker_modules/ribotricer/1.3.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/ribotricer:1.3.2
# docker build src/.docker_modules/ribotricer/1.3.2 -t 'lbmc/ribotricer:1.3.2'
# docker push lbmc/ribotricer:1.3.2
diff --git a/src/.docker_modules/rsem/1.3.0/Dockerfile b/src/.docker_modules/rsem/1.3.0/Dockerfile
index 337521c0496db33c93c20c8fd4d756efcba603a8..b5cdc33b15b0bd7c925cdd7721a0db4d614151d6 100644
--- a/src/.docker_modules/rsem/1.3.0/Dockerfile
+++ b/src/.docker_modules/rsem/1.3.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/rsem/1.3.0/docker_init.sh b/src/.docker_modules/rsem/1.3.0/docker_init.sh
index 56cdc1d97084f3c1623bfb80debbe199fdd3bbd6..961e7c806d22bcb04f1389b6bed6b58ad8a4dbc0 100755
--- a/src/.docker_modules/rsem/1.3.0/docker_init.sh
+++ b/src/.docker_modules/rsem/1.3.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/rsem:1.3.0
# docker build src/.docker_modules/rsem/1.3.0 -t 'lbmc/rsem:1.3.0'
# docker push lbmc/rsem:1.3.0
diff --git a/src/.docker_modules/sabre/039a55e/Dockerfile b/src/.docker_modules/sabre/039a55e/Dockerfile
index f769d43f51f93c949411beea29a540ce2f01a030..5b57fb2458edde5ef8f0f8378cbf25a34e976bdf 100644
--- a/src/.docker_modules/sabre/039a55e/Dockerfile
+++ b/src/.docker_modules/sabre/039a55e/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.12.0
MAINTAINER Lauret Modolo
diff --git a/src/.docker_modules/sabre/039a55e/docker_init.sh b/src/.docker_modules/sabre/039a55e/docker_init.sh
index b5aefa6b8e8b5f34d668c5cd27ef78d763dc1d1d..2cc24edbcfbb3aa1e109d96ff3e39c3cd7689171 100755
--- a/src/.docker_modules/sabre/039a55e/docker_init.sh
+++ b/src/.docker_modules/sabre/039a55e/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/sabre:039a55e
# docker build src/.docker_modules/sabre/039a55e -t 'lbmc/sabre:039a55e'
# docker push lbmc/sabre:039a55e
diff --git a/src/.docker_modules/salmon/0.8.2/Dockerfile b/src/.docker_modules/salmon/0.8.2/Dockerfile
index 31bb28ecce7ec5e5e70baf591ec418a1258bd2dd..34efab530dcbc674555c106850032265e758bb1a 100644
--- a/src/.docker_modules/salmon/0.8.2/Dockerfile
+++ b/src/.docker_modules/salmon/0.8.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/salmon/0.8.2/docker_init.sh b/src/.docker_modules/salmon/0.8.2/docker_init.sh
index 924c7d7b719b4ee22c719519bcb71fcb41091ee4..eeb04828831fc51a64914b649cf0560275f74811 100755
--- a/src/.docker_modules/salmon/0.8.2/docker_init.sh
+++ b/src/.docker_modules/salmon/0.8.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/salmon:0.8.2
# docker build src/.docker_modules/salmon/0.8.2 -t 'lbmc/salmon:0.8.2'
# docker push lbmc/salmon:0.8.2
diff --git a/src/.docker_modules/salmon/1.8.0/Dockerfile b/src/.docker_modules/salmon/1.8.0/Dockerfile
index 065a57e8b363b74e9c8b27d9f12ff144afac56fc..0640748ce1bee26fac53c7c0c74123be5ad354fd 100644
--- a/src/.docker_modules/salmon/1.8.0/Dockerfile
+++ b/src/.docker_modules/salmon/1.8.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
# image: COMBINE-lab/salmon
# This dockerfile is based on the one created by
# Titus Brown (available at https://github.com/ctb/2015-docker-building/blob/master/salmon/Dockerfile)
diff --git a/src/.docker_modules/salmon/1.8.0/docker_init.sh b/src/.docker_modules/salmon/1.8.0/docker_init.sh
index c8bee37c348f09a6d556f5e9f9f37216dbcabe96..2f993148a4cf5f97eacffb001ca008b18417b269 100755
--- a/src/.docker_modules/salmon/1.8.0/docker_init.sh
+++ b/src/.docker_modules/salmon/1.8.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/salmon:1.8.0
docker build src/.docker_modules/salmon/1.8.0 -t 'lbmc/salmon:1.8.0'
docker push lbmc/salmon:1.8.0
diff --git a/src/.docker_modules/sambamba/0.6.7/Dockerfile b/src/.docker_modules/sambamba/0.6.7/Dockerfile
index 5858a176917fc301e165ba18a6d69c34a1bf786a..5500d9de7b4c87f5b114011cba3fd45de2de6aed 100644
--- a/src/.docker_modules/sambamba/0.6.7/Dockerfile
+++ b/src/.docker_modules/sambamba/0.6.7/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/sambamba/0.6.7/docker_init.sh b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
index 07c8d05a978daf9704dd1896adff0306f18cd5ee..f3429f5eb5b8b6742961ce6db5a16fd49f6b7806 100755
--- a/src/.docker_modules/sambamba/0.6.7/docker_init.sh
+++ b/src/.docker_modules/sambamba/0.6.7/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/sambamba:0.6.7
# docker build src/.docker_modules/sambamba/0.6.7 -t 'lbmc/sambamba:0.6.7'
# docker push lbmc/sambamba:0.6.7
diff --git a/src/.docker_modules/sambamba/0.6.9/Dockerfile b/src/.docker_modules/sambamba/0.6.9/Dockerfile
index f45a65412dba77df471e7cd8ee5c79bd2439f1d9..403c03cdd64af029df2701b2d2b683fbe3beaf78 100644
--- a/src/.docker_modules/sambamba/0.6.9/Dockerfile
+++ b/src/.docker_modules/sambamba/0.6.9/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/sambamba/0.6.9/docker_init.sh b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
index 4de76d6617ef8aad1a5bca7748d04b2a747650f1..7bfaa76532722a5fc815b6603b9edd9706334097 100755
--- a/src/.docker_modules/sambamba/0.6.9/docker_init.sh
+++ b/src/.docker_modules/sambamba/0.6.9/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/sambamba:0.6.9
# docker build src/.docker_modules/sambamba/0.6.9 -t 'lbmc/sambamba:0.6.9'
# docker push lbmc/sambamba:0.6.9
diff --git a/src/.docker_modules/samblaster/0.1.24/Dockerfile b/src/.docker_modules/samblaster/0.1.24/Dockerfile
index dcba024b879e8ef7720e35873d9e8101116891c6..95be91482fded2e6d2dbe7d7a3b365547cfa9fcc 100644
--- a/src/.docker_modules/samblaster/0.1.24/Dockerfile
+++ b/src/.docker_modules/samblaster/0.1.24/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/samblaster/0.1.24/docker_init.sh b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
index 319de6666bfb794cf9576204889ec25bc2a885ea..313b99a9ae8ce84cdd6ca9425e9df7fa4ce15cef 100755
--- a/src/.docker_modules/samblaster/0.1.24/docker_init.sh
+++ b/src/.docker_modules/samblaster/0.1.24/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/samblaster:0.1.24
# docker build src/.docker_modules/samblaster/0.1.24 -t 'lbmc/samblaster:0.1.24'
# docker push lbmc/samblaster:0.1.24
diff --git a/src/.docker_modules/samtools/1.11/Dockerfile b/src/.docker_modules/samtools/1.11/Dockerfile
index 054c3e6e421ee3056d43556d6435a23775934ba3..fd70ffa2859f066fa8405adab4f9d391c9a51a34 100644
--- a/src/.docker_modules/samtools/1.11/Dockerfile
+++ b/src/.docker_modules/samtools/1.11/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.8
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/samtools/1.11/docker_init.sh b/src/.docker_modules/samtools/1.11/docker_init.sh
index 273b8472ccb75b1bf1f308fd79f468b72a210797..2428a0ea3c179af9573e472ceaa4e94d9961f3f2 100755
--- a/src/.docker_modules/samtools/1.11/docker_init.sh
+++ b/src/.docker_modules/samtools/1.11/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/samtools:1.11
# docker build src/.docker_modules/samtools/1.11 -t 'lbmc/samtools:1.11'
# docker push lbmc/samtools:1.11
diff --git a/src/.docker_modules/samtools/1.14/Dockerfile b/src/.docker_modules/samtools/1.14/Dockerfile
index 0ea866279e6cd0c0a157acd9da227574c90a1db1..680c4cb04f93e4481f903a3be0e0901d3ad09d19 100644
--- a/src/.docker_modules/samtools/1.14/Dockerfile
+++ b/src/.docker_modules/samtools/1.14/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/samtools:1.14--hb421002_0 AS build
# ldd /usr/local/bin/samtools
diff --git a/src/.docker_modules/samtools/1.14/docker_init.sh b/src/.docker_modules/samtools/1.14/docker_init.sh
index 1d4a215f9637f853bb52b7303772d0f1e64df213..80a0aab7a6be2f38f081764cfc72aa72280838b0 100755
--- a/src/.docker_modules/samtools/1.14/docker_init.sh
+++ b/src/.docker_modules/samtools/1.14/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/samtools:1.14
# docker build src/.docker_modules/samtools/1.14 -t 'lbmc/samtools:1.14'
# docker push lbmc/samtools:1.14
diff --git a/src/.docker_modules/samtools/1.7/Dockerfile b/src/.docker_modules/samtools/1.7/Dockerfile
index 212101a98a9e01783e95d2db93c43d359d5f4d3a..ac8ad4272af8b0c7ca49c2b1fb1e75cbf24efc18 100644
--- a/src/.docker_modules/samtools/1.7/Dockerfile
+++ b/src/.docker_modules/samtools/1.7/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM alpine:3.8
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/samtools/1.7/docker_init.sh b/src/.docker_modules/samtools/1.7/docker_init.sh
index 5839d04f8ce5da781ec4f0772b712e78ca47eea7..68f4d2dd429d30bf905a097231764b97b1ed230e 100755
--- a/src/.docker_modules/samtools/1.7/docker_init.sh
+++ b/src/.docker_modules/samtools/1.7/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/samtools:1.7
# docker build src/.docker_modules/samtools/1.7 -t 'lbmc/samtools:1.7'
# docker push lbmc/samtools:1.7
diff --git a/src/.docker_modules/sanity/Dockerfile b/src/.docker_modules/sanity/Dockerfile
index 99f9545ea137d6a7450983b9719301c7e7edf578..097acd14f8fec63a9add0c8a071800ec3090b9aa 100644
--- a/src/.docker_modules/sanity/Dockerfile
+++ b/src/.docker_modules/sanity/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
##### BASE IMAGE #####
FROM ubuntu:18.04
diff --git a/src/.docker_modules/sanity/docker_init.sh b/src/.docker_modules/sanity/docker_init.sh
index 598a32d8cf81ec5d395021d927eea1ffc45bb126..cff77d36bed62c485f7db6e65b1b01dd9864fa92 100755
--- a/src/.docker_modules/sanity/docker_init.sh
+++ b/src/.docker_modules/sanity/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull mlepetit/sanity
docker build src/.docker_modules/sanity -t 'lbmc/sanity'
docker push lbmc/sanity
diff --git a/src/.docker_modules/seqkit/2.1.0/Dockerfile b/src/.docker_modules/seqkit/2.1.0/Dockerfile
index 72fa012b04ddf31809f2fcd4b0d8576e545f39b5..cb03ca617bcc7154d3a63f050558aece8515fbfb 100644
--- a/src/.docker_modules/seqkit/2.1.0/Dockerfile
+++ b/src/.docker_modules/seqkit/2.1.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:16.04
#Begin: install prerequisites
diff --git a/src/.docker_modules/seqkit/2.1.0/docker_init.sh b/src/.docker_modules/seqkit/2.1.0/docker_init.sh
index c4b8240237ec02887f7665a8ed8e586a313cbc92..1afb61e2a81ea85fa8f4fcaa72cd6d0c58dc9ac0 100755
--- a/src/.docker_modules/seqkit/2.1.0/docker_init.sh
+++ b/src/.docker_modules/seqkit/2.1.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/seqkit:2.1.0
docker build src/.docker_modules/seqkit/2.1.0 -t 'lbmc/seqkit:2.1.0'
docker push lbmc/seqkit:2.1.0
diff --git a/src/.docker_modules/sratoolkit/2.8.2/Dockerfile b/src/.docker_modules/sratoolkit/2.8.2/Dockerfile
index 55622ef79ad427763d9f8e6e1523d405906835c9..f7b8661b04b6436921caaeb011334c7f308b3d82 100644
--- a/src/.docker_modules/sratoolkit/2.8.2/Dockerfile
+++ b/src/.docker_modules/sratoolkit/2.8.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
index d6207d7eca02771e2d9569e7ce43829908cc473f..240405f599f28d2e40f9e87db2d65135f95aa3cf 100755
--- a/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
+++ b/src/.docker_modules/sratoolkit/2.8.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/sratoolkit:2.8.2
# docker build src/.docker_modules/sratoolkit/2.8.2 -t 'lbmc/sratoolkit:2.8.2'
# docker push lbmc/sratoolkit:2.8.2
diff --git a/src/.docker_modules/sratoolkit/3.0.0/Dockerfile b/src/.docker_modules/sratoolkit/3.0.0/Dockerfile
index 79e631b0fdb4dae687e7a2e0904c7169945d8e02..f4b073df5c028d587321cd040a54a6dd8c5cbfea 100644
--- a/src/.docker_modules/sratoolkit/3.0.0/Dockerfile
+++ b/src/.docker_modules/sratoolkit/3.0.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ncbi/sra-tools:3.0.0
ENV SRATOOLKIT_VERSION=3.0.0
diff --git a/src/.docker_modules/sratoolkit/3.0.0/docker_init.sh b/src/.docker_modules/sratoolkit/3.0.0/docker_init.sh
index 0426a71ecd47b13c6c7d56b379899fc80a125e2b..7cc784c2cbde76eebaa03fdce5e0656e07467abc 100755
--- a/src/.docker_modules/sratoolkit/3.0.0/docker_init.sh
+++ b/src/.docker_modules/sratoolkit/3.0.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/sratoolkit:3.0.0
# docker build src/.docker_modules/sratoolkit/3.0.0 -t 'lbmc/sratoolkit:3.0.0'
# docker push lbmc/sratoolkit:3.0.0
diff --git a/src/.docker_modules/star/2.5.3/Dockerfile b/src/.docker_modules/star/2.5.3/Dockerfile
index a045a2352dd59dc8de04e07b233a0399b891cde8..8a25919ae2a17ba6892d443888bc658ba6772bb2 100644
--- a/src/.docker_modules/star/2.5.3/Dockerfile
+++ b/src/.docker_modules/star/2.5.3/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/star:2.7.3a--0
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/star/2.5.3/docker_init.sh b/src/.docker_modules/star/2.5.3/docker_init.sh
index 791f2b21442a6deefb0538a26b3f23f43b841a40..eb44fb873aa9c1a5ae33464fc02b9904e4ee23ab 100755
--- a/src/.docker_modules/star/2.5.3/docker_init.sh
+++ b/src/.docker_modules/star/2.5.3/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/star:2.7.3a
# docker build src/.docker_modules/star/2.7.3a/ -t 'lbmc/star:2.7.3a'
# docker push lbmc/star:2.7.3a
diff --git a/src/.docker_modules/star/2.7.3a/Dockerfile b/src/.docker_modules/star/2.7.3a/Dockerfile
index a045a2352dd59dc8de04e07b233a0399b891cde8..8a25919ae2a17ba6892d443888bc658ba6772bb2 100644
--- a/src/.docker_modules/star/2.7.3a/Dockerfile
+++ b/src/.docker_modules/star/2.7.3a/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/star:2.7.3a--0
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/star/2.7.3a/docker_init.sh b/src/.docker_modules/star/2.7.3a/docker_init.sh
index 791f2b21442a6deefb0538a26b3f23f43b841a40..eb44fb873aa9c1a5ae33464fc02b9904e4ee23ab 100755
--- a/src/.docker_modules/star/2.7.3a/docker_init.sh
+++ b/src/.docker_modules/star/2.7.3a/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/star:2.7.3a
# docker build src/.docker_modules/star/2.7.3a/ -t 'lbmc/star:2.7.3a'
# docker push lbmc/star:2.7.3a
diff --git a/src/.docker_modules/stringtie/2.1.1/Dockerfile b/src/.docker_modules/stringtie/2.1.1/Dockerfile
index 7e0f2a18d02ced44dcbd2ee99cede00df6c1d0fe..3a09d8436f49a23bb657deab0b2afa4fa70e6101 100644
--- a/src/.docker_modules/stringtie/2.1.1/Dockerfile
+++ b/src/.docker_modules/stringtie/2.1.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:16.04
Maintainer Chen Yuelong <yuelong.chen.btr@gmail.com>
diff --git a/src/.docker_modules/stringtie/2.1.1/docker_init.sh b/src/.docker_modules/stringtie/2.1.1/docker_init.sh
index eadefe1d5355836a1b8984820477bfe628042650..665d78c44325670c0d4879f63d95a5a8f0f04911 100755
--- a/src/.docker_modules/stringtie/2.1.1/docker_init.sh
+++ b/src/.docker_modules/stringtie/2.1.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/stringtie:2.1.1
docker build src/.docker_modules/stringtie/2.1.1 -t 'lbmc/stringtie:2.1.1'
docker push lbmc/stringtie:2.1.1
diff --git a/src/.docker_modules/subread/1.6.4/Dockerfile b/src/.docker_modules/subread/1.6.4/Dockerfile
index 97d5870ad4d7a59ec0e8f38300d8e86651cc2e8b..76decf4026d880bb4bab96431ecccbc9251c8510 100644
--- a/src/.docker_modules/subread/1.6.4/Dockerfile
+++ b/src/.docker_modules/subread/1.6.4/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/subread:1.6.4--h84994c4_1
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/subread/1.6.4/docker_init.sh b/src/.docker_modules/subread/1.6.4/docker_init.sh
index 5d7740e939fb1aaae30de4bf836d9422f52430d0..be1c934f801f442c17f7242d776346846e1d56bd 100755
--- a/src/.docker_modules/subread/1.6.4/docker_init.sh
+++ b/src/.docker_modules/subread/1.6.4/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/subread:1.6.4
# docker build src/.docker_modules/subread/1.6.4 -t 'lbmc/subread:1.6.4'
# docker push lbmc/subread:1.6.4
diff --git a/src/.docker_modules/tinycov/0.3.1/Dockerfile b/src/.docker_modules/tinycov/0.3.1/Dockerfile
index 588d7b244cd0e40376e344bde1f168f5883c2e17..417824e8d14f2e9804d77144daf56342a14c157b 100644
--- a/src/.docker_modules/tinycov/0.3.1/Dockerfile
+++ b/src/.docker_modules/tinycov/0.3.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM python:3.9-slim
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/tinycov/0.3.1/docker_init.sh b/src/.docker_modules/tinycov/0.3.1/docker_init.sh
index 87cf4fff860154170d626c7fbaf4888cd8ae5678..3c54e25a0dd69759b99700048e8fea21154cc5e4 100755
--- a/src/.docker_modules/tinycov/0.3.1/docker_init.sh
+++ b/src/.docker_modules/tinycov/0.3.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/tinycov:0.3.1
docker build src/.docker_modules/tinycov/0.3.1 -t 'lbmc/tinycov:0.3.1'
docker push lbmc/tinycov:0.3.1
diff --git a/src/.docker_modules/tophat/2.1.1/Dockerfile b/src/.docker_modules/tophat/2.1.1/Dockerfile
index 3c34d4641239ebfa7cbb65a716e436f2e0c099ee..b2fc8652769ee7c76b10cabedfe1dc44d7a4a29a 100644
--- a/src/.docker_modules/tophat/2.1.1/Dockerfile
+++ b/src/.docker_modules/tophat/2.1.1/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/tophat/2.1.1/docker_init.sh b/src/.docker_modules/tophat/2.1.1/docker_init.sh
index f14f6b0bc911c97eedf3af71393df55126403fbe..9cf90bd6ef0154bb16b1bb2565910e5ebaa540a5 100755
--- a/src/.docker_modules/tophat/2.1.1/docker_init.sh
+++ b/src/.docker_modules/tophat/2.1.1/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/tophat:2.1.1
# docker build src/.docker_modules/tophat/2.1.1 -t 'lbmc/tophat:2.1.1'
# docker push lbmc/tophat:2.1.1
diff --git a/src/.docker_modules/trimmomatic/0.36/Dockerfile b/src/.docker_modules/trimmomatic/0.36/Dockerfile
index 8e04269a05b905fa41c17fe86338bce8f75b33c0..39a94d65cb2cb89ec4431740524346ae71c07586 100644
--- a/src/.docker_modules/trimmomatic/0.36/Dockerfile
+++ b/src/.docker_modules/trimmomatic/0.36/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/trimmomatic/0.36/docker_init.sh b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
index 34477452f757308c8cc65862b10310ae2076c5fc..140889957df2f245a91db670055cd2d8cfa0bc4e 100755
--- a/src/.docker_modules/trimmomatic/0.36/docker_init.sh
+++ b/src/.docker_modules/trimmomatic/0.36/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/trimmomatic:0.36
# docker build src/.docker_modules/trimmomatic/0.36 -t 'lbmc/trimmomatic:0.36'
# docker push lbmc/trimmomatic:0.36
diff --git a/src/.docker_modules/trinity/2.13.2/Dockerfile b/src/.docker_modules/trinity/2.13.2/Dockerfile
index f8fdc554960b16f4cb32d7ad6e40e8768cdafa0a..81aa71402de1a8b0e377c463fd670218984387d3 100644
--- a/src/.docker_modules/trinity/2.13.2/Dockerfile
+++ b/src/.docker_modules/trinity/2.13.2/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/trinity:2.13.2--ha140323_0
ENV TRINITY_VERSION=2.13.2--ha140323_0
diff --git a/src/.docker_modules/trinity/2.13.2/docker_init.sh b/src/.docker_modules/trinity/2.13.2/docker_init.sh
index ff9da019a0dc0f6a305e1295720ba735cb0bc94b..8f5037c74cb25f6b96edbe2facf1b8d98ead7cc7 100755
--- a/src/.docker_modules/trinity/2.13.2/docker_init.sh
+++ b/src/.docker_modules/trinity/2.13.2/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/trinity:2.13.2
docker build src/.docker_modules/trinity/2.13.2 -t 'lbmc/trinity:2.13.2'
docker push lbmc/trinity:2.13.2
diff --git a/src/.docker_modules/ucsc/375/Dockerfile b/src/.docker_modules/ucsc/375/Dockerfile
index 9365a974bdc86f80897ad97ca8d13436b3bb364d..345c9ee5670f2c924170501f5bcb74bf95a2525f 100644
--- a/src/.docker_modules/ucsc/375/Dockerfile
+++ b/src/.docker_modules/ucsc/375/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:jessie
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/ucsc/375/docker_init.sh b/src/.docker_modules/ucsc/375/docker_init.sh
index 5f3b3913b2a62e5151f1260d9662749268c3c16f..8f130a46683ec36dbb95696348e23721e1a49a34 100755
--- a/src/.docker_modules/ucsc/375/docker_init.sh
+++ b/src/.docker_modules/ucsc/375/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/ucsc:375
# docker build src/.docker_modules/ucsc/375/ -t 'lbmc/ucsc:375'
# docker push lbmc/ucsc:375
diff --git a/src/.docker_modules/ucsc/400/Dockerfile b/src/.docker_modules/ucsc/400/Dockerfile
index 6409f862f0c1b51d853597cd4404bb55f03137c2..c509434a8d634796c68eb59e09147db5e0d7e2d2 100644
--- a/src/.docker_modules/ucsc/400/Dockerfile
+++ b/src/.docker_modules/ucsc/400/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:jessie
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/ucsc/400/docker_init.sh b/src/.docker_modules/ucsc/400/docker_init.sh
index df1e3e58fbb36aa4cce0c1ecec4e550827a200ed..2ac97cad48fb86da00f2c0d2c2bb12c0a7e0fda0 100755
--- a/src/.docker_modules/ucsc/400/docker_init.sh
+++ b/src/.docker_modules/ucsc/400/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/ucsc:400
# docker build src/.docker_modules/ucsc/400/ -t 'lbmc/ucsc:400'
# docker push lbmc/ucsc:400
diff --git a/src/.docker_modules/ucsc/407/Dockerfile b/src/.docker_modules/ucsc/407/Dockerfile
index 76eb05edcb7ac5fc84ef82251b037f9882e188d8..89e0b23fd9084e16f90579d381d465b4520bd335 100644
--- a/src/.docker_modules/ucsc/407/Dockerfile
+++ b/src/.docker_modules/ucsc/407/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:jessie
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/ucsc/407/bedgraph_to_wig.pl b/src/.docker_modules/ucsc/407/bedgraph_to_wig.pl
index 19fe222598db78fcf6a2e0c4fdb1ad270f0549da..9cb1bb7e6e590ae40d3e6625e8534e170a6c9267 100644
--- a/src/.docker_modules/ucsc/407/bedgraph_to_wig.pl
+++ b/src/.docker_modules/ucsc/407/bedgraph_to_wig.pl
@@ -1,5 +1,9 @@
#!/usr/bin/perl
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
# Description: This script converts bedGraph to fixedStep wig format with defined step size. Input file may be compressed as .gz.
# Coordinates in bedGraph input are assumed to be 0-based (http://genome.ucsc.edu/goldenPath/help/bedgraph.html).
# Coordinates in wig output are 1-based (http://genome.ucsc.edu/goldenPath/help/wiggle.html).
diff --git a/src/.docker_modules/ucsc/407/docker_init.sh b/src/.docker_modules/ucsc/407/docker_init.sh
index a68b313b07b5a55ed904be8de364493f09e26a36..b3c2cd7444474076d674849d0b56464954f63ed5 100755
--- a/src/.docker_modules/ucsc/407/docker_init.sh
+++ b/src/.docker_modules/ucsc/407/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/ucsc:407
# docker build src/.docker_modules/ucsc/407/ -t 'lbmc/ucsc:407'
# docker push lbmc/ucsc:407
diff --git a/src/.docker_modules/ucsc/407/gtf2bed.pl b/src/.docker_modules/ucsc/407/gtf2bed.pl
index c6ab16407e0ac5ac47d5de6a9fe5dcfd6104a360..1fa505f1642be3e5c16459ccd4edcac2bef4b81b 100644
--- a/src/.docker_modules/ucsc/407/gtf2bed.pl
+++ b/src/.docker_modules/ucsc/407/gtf2bed.pl
@@ -1,26 +1,9 @@
#!/usr/bin/perl
# Copyright (c) 2011 Erik Aronesty (erik@q32.com)
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ALSO, IT WOULD BE NICE IF YOU LET ME KNOW YOU USED IT.
+# SPDX-License-Identifier: AGPL-3.0-or-later
use Getopt::Long;
diff --git a/src/.docker_modules/umi_tools/0.5.4/Dockerfile b/src/.docker_modules/umi_tools/0.5.4/Dockerfile
index 81c4cc8c1529187fd8c34f5106f05e2ba6b55be6..dbcd16347c783c874274fa3fa8070bd1928d7d27 100644
--- a/src/.docker_modules/umi_tools/0.5.4/Dockerfile
+++ b/src/.docker_modules/umi_tools/0.5.4/Dockerfile
@@ -1,2 +1,6 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM quay.io/biocontainers/umi_tools:0.5.4--py27hdd9f355_1
MAINTAINER Rémi SERAPHIN
diff --git a/src/.docker_modules/umi_tools/0.5.4/docker_init.sh b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
index 4c669f326f8092d92f372b65f43df77d8e14fc4e..77591ae15a834a8567ee5457e31704a317e90a54 100755
--- a/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
+++ b/src/.docker_modules/umi_tools/0.5.4/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/umi_tools:1.0.0
# docker build src/.docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
# docker push lbmc/umi_tools:1.0.0
diff --git a/src/.docker_modules/umi_tools/1.0.0/Dockerfile b/src/.docker_modules/umi_tools/1.0.0/Dockerfile
index d82cc9a6c7dc0877522149912b09899f7879ede9..3664a0b11016aeffdc63db645d4a1a1ee1e25b1c 100644
--- a/src/.docker_modules/umi_tools/1.0.0/Dockerfile
+++ b/src/.docker_modules/umi_tools/1.0.0/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM debian:stretch
MAINTAINER Rémi SERAPHIN
diff --git a/src/.docker_modules/umi_tools/1.0.0/docker_init.sh b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
index 4c669f326f8092d92f372b65f43df77d8e14fc4e..77591ae15a834a8567ee5457e31704a317e90a54 100755
--- a/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
+++ b/src/.docker_modules/umi_tools/1.0.0/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/umi_tools:1.0.0
# docker build src/.docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
# docker push lbmc/umi_tools:1.0.0
diff --git a/src/.docker_modules/urqt/d62c1f8/Dockerfile b/src/.docker_modules/urqt/d62c1f8/Dockerfile
index 9b54a7eb91ad3767532c8703fe25d6cad29e27cb..07c07ac58c1df937536a9b45bf3f027a634f19d6 100644
--- a/src/.docker_modules/urqt/d62c1f8/Dockerfile
+++ b/src/.docker_modules/urqt/d62c1f8/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/urqt/d62c1f8/docker_init.sh b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
index 5bc22f778169ec31e6b391d1d6cdfdc6f2d99f04..3d0c791afd915980f01aab04543856bc600e5229 100755
--- a/src/.docker_modules/urqt/d62c1f8/docker_init.sh
+++ b/src/.docker_modules/urqt/d62c1f8/docker_init.sh
@@ -1,4 +1,9 @@
#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
docker pull lbmc/urqt:d62c1f8
# docker build src/.docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
# docker push lbmc/urqt:d62c1f8
diff --git a/src/example_chipseq.nf b/src/example_chipseq.nf
index 454617c9c6fa21b9cdd2c8fd378bbcd7c60ea42e..e443c2bd7e3cf0dc2fba49345b42d2d166156592 100644
--- a/src/example_chipseq.nf
+++ b/src/example_chipseq.nf
@@ -1,3 +1,6 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
nextflow.enable.dsl=2
diff --git a/src/example_marseq.nf b/src/example_marseq.nf
index 8e31a26b0d1b8f293880ae95c07d83dfb273511e..cc6fa4f77e1140d6424ce282d7638e6166c68987 100644
--- a/src/example_marseq.nf
+++ b/src/example_marseq.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
nextflow.enable.dsl=2
/*
diff --git a/src/example_variant_calling.nf b/src/example_variant_calling.nf
index 5d793ed4898ac89753b2188f252403f903182043..61b3d88d7e42c7cee18c061dd257a87b931c928b 100644
--- a/src/example_variant_calling.nf
+++ b/src/example_variant_calling.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
nextflow.enable.dsl=2
/*
diff --git a/src/fasta_sampler.nf b/src/fasta_sampler.nf
index d1200ed496c77756cde525835f581b71b2528990..b6f4ef252ea58d101a1f5d7d1102eaa54de028c7 100644
--- a/src/fasta_sampler.nf
+++ b/src/fasta_sampler.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
Channel
.fromPath( "data/tiny_dataset/fasta/*.fasta" )
.set { fasta_file }
diff --git a/src/in2p3.pbs b/src/in2p3.pbs
index 0fed278f5dde68330b7c721ca4e5896c08dd8c19..710c9dae2dc6d5ce4c49063c3288b0326dbd3783 100644
--- a/src/in2p3.pbs
+++ b/src/in2p3.pbs
@@ -1,5 +1,9 @@
#!/bin/sh
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
#SBATCH --job-name=nextflow
#SBATCH --ntasks=1
diff --git a/src/install_nextflow.sh b/src/install_nextflow.sh
index 272c24929f856970e80f8cd8739fea8754ae9f6c..612f836fec64180cdfc8e36c46b5e17291dd1276 100755
--- a/src/install_nextflow.sh
+++ b/src/install_nextflow.sh
@@ -1,4 +1,8 @@
#!/bin/sh
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
java -version
curl -s https://get.nextflow.io | bash
diff --git a/src/nextflow.config b/src/nextflow.config
index 02701889fec6c0910293425418e4c3e9c3cf7436..f36e54cfe1c943e8f2eb42329d3490b8397ff7ca 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
nextflowVersion = '>=20'
manifest {
diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf
index e2d832e72b97340f1a0811dde6358bd73cb2e606..5d8a6d66a40caa8892cd26cb9ef42f6460660865 100644
--- a/src/nf_modules/agat/main.nf
+++ b/src/nf_modules/agat/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.8.0"
container_url = "lbmc/agat:${version}"
diff --git a/src/nf_modules/alntools/main.nf b/src/nf_modules/alntools/main.nf
index 19ee7b096f8f8aa40f7c57602caee4060f17227a..dc6d01825633d5203fa478115b2bb0cccaace626 100644
--- a/src/nf_modules/alntools/main.nf
+++ b/src/nf_modules/alntools/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "dd96682"
container_url = "lbmc/alntools:${version}"
diff --git a/src/nf_modules/beagle/main.nf b/src/nf_modules/beagle/main.nf
index bc0a54b21d941d358d047334c29d67f4b55be16b..c428450509ad2cc75d4d834dc6f859d29a0d8be2 100644
--- a/src/nf_modules/beagle/main.nf
+++ b/src/nf_modules/beagle/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "5.1_24Aug19.3e8--hdfd78af_1"
container_url = "quay.io/biocontainers/beagle::${version}"
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index 674a9621d9856a4fb0ccb6123ed91db2386d537c..4b7225d53b8f6457ef2f3a3719913cb54efc42ee 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.25.0"
container_url = "lbmc/bedtools:${version}"
diff --git a/src/nf_modules/bioawk/main.nf b/src/nf_modules/bioawk/main.nf
index eaa5a4a2e50a1e9244f99ae6cc9fb10401bfb5a9..4c56dee0890ca116fbf4fc5dfc4a2f0cf4ea208c 100644
--- a/src/nf_modules/bioawk/main.nf
+++ b/src/nf_modules/bioawk/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "1.0"
container_url = "lbmc/bioawk:${version}"
diff --git a/src/nf_modules/bioconvert/main.nf b/src/nf_modules/bioconvert/main.nf
index 884ebb9ee693b27fca4cda7724ca3145476ec60f..494323c21a32f857e270c499f361668617a963af 100644
--- a/src/nf_modules/bioconvert/main.nf
+++ b/src/nf_modules/bioconvert/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.4.0"
container_url = "lbmc/bioconvert:${version}"
params.bigwig_to_wig = ""
diff --git a/src/nf_modules/bowtie/main.nf b/src/nf_modules/bowtie/main.nf
index a841fc36195dabcf2bb238431680f9e0677aa701..bffdb7847545231a06ccd47dbad193d501ba7e40 100644
--- a/src/nf_modules/bowtie/main.nf
+++ b/src/nf_modules/bowtie/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "1.2.2"
container_url = "lbmc/bowtie:${version}"
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index 3a0fc967f381ee84f40cd7a4ac3887bcb32d70ed..72881a9e9134c90c4c373360930ecc7c54f8a547 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.3.4.1"
container_url = "lbmc/bowtie2:${version}"
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 0490b082a4d71d8cef7aa68d44ccf96d2ea41d89..f6a489844aaaa3b74cf7a5e23cd2f91cb1015f24 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.7.17"
container_url = "lbmc/bwa:${version}"
diff --git a/src/nf_modules/cellphonedb/main.nf b/src/nf_modules/cellphonedb/main.nf
index 37fb970082ea2f04a9225f8876b726dd93dee78b..086a636d5b2a2603dab43a1ef8055df0e31efef0 100644
--- a/src/nf_modules/cellphonedb/main.nf
+++ b/src/nf_modules/cellphonedb/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "3.0.0"
container_url = "mlepetit/cellphonedb:latest"
diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf
index 8d93b2ae9bb160ed62969348b12e5f6834df2eb4..984af010a07af48f6a042404d50e026be7ce13c3 100644
--- a/src/nf_modules/cutadapt/main.nf
+++ b/src/nf_modules/cutadapt/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.1"
container_url = "lbmc/cutadapt:${version}"
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 81d8b836f015ef21991d217e2c214099bd925ba7..ce1563b895f6f46fb6349934d1afc945f9a643c1 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "v2.2.2_cv3"
container_url = "biocontainers/danpos:${version}"
diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index 97e4027de2f91930c5fd227c29b0b563b9f3c027..49c30e5898ab2b21d5329be2be0579ca7e05cda3 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/src/nf_modules/deeptools/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "3.5.1"
container_url = "lbmc/deeptools:${version}"
diff --git a/src/nf_modules/emase-zero/main.nf b/src/nf_modules/emase-zero/main.nf
index 87c5020d38950cbfe8618aa2fc9ed839492e6aac..f5bad763c953acac17d6199b1e5ef38b1975dfc3 100644
--- a/src/nf_modules/emase-zero/main.nf
+++ b/src/nf_modules/emase-zero/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.3.1"
container_url = "lbmc/emase-zero:${version}"
diff --git a/src/nf_modules/emase/main.nf b/src/nf_modules/emase/main.nf
index 4388aad7656b1d648ac53398b3f99de1791b387a..4b3b46fda021483b5b8a871959176a85cda7fb04 100644
--- a/src/nf_modules/emase/main.nf
+++ b/src/nf_modules/emase/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.10.16"
container_url = "lbmc/emase:${version}"
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index dc26ead41fca546e323a8952726e6ac386f8b68a..4b6991fbc88e39a1b373180197e1f9317280028a 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.23.2"
container_url = "lbmc/fastp:${version}"
diff --git a/src/nf_modules/fastqc/main.nf b/src/nf_modules/fastqc/main.nf
index da0c7bc7c952a7c4161751eef34fcfcf1882d2bd..7ecacc4ee61ca33ffe4c6dbc88b00c0e3f3e34e3 100644
--- a/src/nf_modules/fastqc/main.nf
+++ b/src/nf_modules/fastqc/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.11.5"
container_url = "lbmc/fastqc:${version}"
diff --git a/src/nf_modules/flexi_splitter/main.nf b/src/nf_modules/flexi_splitter/main.nf
index 753ef1be2fd8586645c09ddde2d29342b7e5c103..95636c708ec27e7f36162746b35d6a99e73a10da 100644
--- a/src/nf_modules/flexi_splitter/main.nf
+++ b/src/nf_modules/flexi_splitter/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "1.0.2"
container_url = "lbmc/flexi_splitter:${version}"
diff --git a/src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml b/src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
index 72f46d2dc1833e1fab00b734aefadd55a70b44c1..28449772387ae91999658b5471c5f71822b5f7e5 100644
--- a/src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
+++ b/src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
PLATE:
coords:
reads: 0
diff --git a/src/nf_modules/flexi_splitter/toy_file_paired.yaml b/src/nf_modules/flexi_splitter/toy_file_paired.yaml
index dec6e8c4df34121693f591fd68f49dc8f787e7d4..164a4501a372ed2e91f35cb433747a71f855ef14 100644
--- a/src/nf_modules/flexi_splitter/toy_file_paired.yaml
+++ b/src/nf_modules/flexi_splitter/toy_file_paired.yaml
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
PCR:
coords:
reads: 3
diff --git a/src/nf_modules/g2gtools/main.nf b/src/nf_modules/g2gtools/main.nf
index 15af58850fac947d903eec5b3459a4eb90b8b09d..650c2f3c58819e70435e93fa16862698af8b90eb 100644
--- a/src/nf_modules/g2gtools/main.nf
+++ b/src/nf_modules/g2gtools/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.2.8"
container_url = "lbmc/g2gtools:${version}"
diff --git a/src/nf_modules/gatk3/main.nf b/src/nf_modules/gatk3/main.nf
index 35a1ab7a479b41da6480535364c5caeca1c12e34..0acc35723b7707baf74393b3f8e5e24f9263a329 100644
--- a/src/nf_modules/gatk3/main.nf
+++ b/src/nf_modules/gatk3/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "3.8.0"
container_url = "lbmc/gatk:${version}"
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 885b3211f0586cdb7fa52a307b090bc3328b739f..9fb770d0a07ac6c93c95e6be4689ace9e9b3fc71 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "4.2.0.0"
container_url = "broadinstitute/gatk:${version}"
diff --git a/src/nf_modules/gffread/main.nf b/src/nf_modules/gffread/main.nf
index 01bbf5d1d61b6462b5390a23ad16c457a5ef46a0..ec37027f3c9339a4e274a9939228f130c48b16fd 100644
--- a/src/nf_modules/gffread/main.nf
+++ b/src/nf_modules/gffread/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.12.2"
container_url = "lbmc/gffread:${version}"
diff --git a/src/nf_modules/guppy-cpu/main.nf b/src/nf_modules/guppy-cpu/main.nf
index 36a15eaa582f5a6ac52ab8cde52576e49421a598..19aca488c72b185e75f90040f38e83fac8a37a3b 100644
--- a/src/nf_modules/guppy-cpu/main.nf
+++ b/src/nf_modules/guppy-cpu/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "5.0.11"
container_url = "lbmc/guppy-cpu:${version}"
diff --git a/src/nf_modules/guppy-gpu/main.nf b/src/nf_modules/guppy-gpu/main.nf
index 34e8fb5b80e7b66a03e7877dcbe470d3ee69b563..c8f72d11589032d9f4f5aba844eba3a37f18f815 100644
--- a/src/nf_modules/guppy-gpu/main.nf
+++ b/src/nf_modules/guppy-gpu/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "5.0.11"
container_url = "lbmc/guppy-gpu:${version}"
diff --git a/src/nf_modules/hisat2/main.nf b/src/nf_modules/hisat2/main.nf
index 24c317ed1fa8257ae69230bb27d3ccbff707c82a..294bf2e260fd199af717460302e758500e4ac6b8 100644
--- a/src/nf_modules/hisat2/main.nf
+++ b/src/nf_modules/hisat2/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.2.1"
container_url = "lbmc/hisat2:${version}"
diff --git a/src/nf_modules/htseq/main.nf b/src/nf_modules/htseq/main.nf
index 93377467bc8cc61c3c7fad459c51bc253737be2e..fe4143c99845131832bc70b50e781cba5d8ef63d 100644
--- a/src/nf_modules/htseq/main.nf
+++ b/src/nf_modules/htseq/main.nf
@@ -1,3 +1,6 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
version = "1.99.2"
container_url = "lbmc/htseq:${version}"
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 8d3fe1d3a9bbdd1435863f93ab0b74c1d7bcd994..89201c3847febd0be3595662754308c9bc0b27c4 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.44.0"
container_url = "lbmc/kallisto:${version}"
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index 6edfa13080ac635bf7917b4013eeccad9265d910..3f5520b9bb331477e4e52a760002ead24eb21d90 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.26.0"
container_url = "lbmc/kb:${version}"
diff --git a/src/nf_modules/macs2/main.nf b/src/nf_modules/macs2/main.nf
index 51bed4bebf4060e71f5532fb9ac83fdd89b24231..05d5938dc16c784f0c40b6a9e4cb488767d83a5e 100644
--- a/src/nf_modules/macs2/main.nf
+++ b/src/nf_modules/macs2/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.1.2"
container_url = "lbmc/macs2:${version}"
diff --git a/src/nf_modules/macs3/main.nf b/src/nf_modules/macs3/main.nf
index b8c2dbcebac257a7ff63f85d3737b48a97f648c2..42cae0637d74057c569c0c13ff91a8e50305885f 100644
--- a/src/nf_modules/macs3/main.nf
+++ b/src/nf_modules/macs3/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "3.0.0a6"
container_url = "lbmc/macs3:${version}"
diff --git a/src/nf_modules/minimap2/main.nf b/src/nf_modules/minimap2/main.nf
index 9dbe5a575f840d9b911f778b7adf039747a6024f..311a742d8582b6fa1cdbd26e425ac24ad6cd2fbd 100644
--- a/src/nf_modules/minimap2/main.nf
+++ b/src/nf_modules/minimap2/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.17"
container_url = "lbmc/minimap2:${version}"
diff --git a/src/nf_modules/multiqc/main.nf b/src/nf_modules/multiqc/main.nf
index 755ae0212662f241acd1202593ba383541d74551..cbdff9e89fe71ec7dfa80bc204673a6e06fd40c1 100644
--- a/src/nf_modules/multiqc/main.nf
+++ b/src/nf_modules/multiqc/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
// multiqc generate nice html report combining lots of differents bioinformatics
// tools report.
//
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
index faaa78c1e35c9b59f5f60e7982e9451178c7a032..20fe2d272ab35996dff59734ce1bf3f87d2675e0 100644
--- a/src/nf_modules/picard/main.nf
+++ b/src/nf_modules/picard/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.18.11"
container_url = "lbmc/picard:${version}"
diff --git a/src/nf_modules/porechop/main.nf b/src/nf_modules/porechop/main.nf
index b90075efdbc6b83eaf7994a70378ad72b1967a01..3c6e777c1176000786d15317559ca9c8e3dce3b0 100644
--- a/src/nf_modules/porechop/main.nf
+++ b/src/nf_modules/porechop/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.2.4"
container_url = "lbmc/porechop:${version}"
diff --git a/src/nf_modules/rasusa/main.nf b/src/nf_modules/rasusa/main.nf
index 4a671d0c34d8bff59dbe776e4d7896148f711b71..a04f3721986c218b384e0424c0fd7250a4719f15 100644
--- a/src/nf_modules/rasusa/main.nf
+++ b/src/nf_modules/rasusa/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.6.0"
container_url = "lbmc/rasusa:${version}"
diff --git a/src/nf_modules/rasusa/test.nf b/src/nf_modules/rasusa/test.nf
index 261e374bbbcd934c1992f844448884f915bc29ab..dbe73a23c6f8cf4008c06113c385da3e409808c1 100644
--- a/src/nf_modules/rasusa/test.nf
+++ b/src/nf_modules/rasusa/test.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
nextflow.enable.dsl=2
/*
diff --git a/src/nf_modules/rasusa/test.sh b/src/nf_modules/rasusa/test.sh
index d66e26f2a334fe43a43b3228b270046d0dbed66c..218887e758bc8b74af1768d55bb2ba8324becf4b 100644
--- a/src/nf_modules/rasusa/test.sh
+++ b/src/nf_modules/rasusa/test.sh
@@ -1,4 +1,9 @@
#! /bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq"
./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" --coverage 1.0
./nextflow src/nf_modules/rasusa/test.nf -c src/nextflow.config -profile docker --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --fastq "data/tiny_dataset/fastq/tiny_R1.fastq" --size "1Mb"
\ No newline at end of file
diff --git a/src/nf_modules/salmon/main.nf b/src/nf_modules/salmon/main.nf
index 860d210b41127c4c2f0a2f6625dd4b35420ca85f..cb685268a9eacfda2208a8f664b7235e99e00457 100644
--- a/src/nf_modules/salmon/main.nf
+++ b/src/nf_modules/salmon/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "1.8.0"
container_url = "lbmc/salmon:${version}"
diff --git a/src/nf_modules/sambamba/main.nf b/src/nf_modules/sambamba/main.nf
index ea6c6e972bf3e0360df35c2b6eeb9ad227d42450..0e295c9e82cc93a214c1be79dae81fc74a1360fd 100644
--- a/src/nf_modules/sambamba/main.nf
+++ b/src/nf_modules/sambamba/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "0.6.7"
container_url = "lbmc/sambamba:${version}"
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index ed88dc56dfeaa239845c7f1f8467bfc1d81624eb..29136421832b8d747f3137957e6c2c859a9026b2 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "1.11"
container_url = "lbmc/samtools:${version}"
diff --git a/src/nf_modules/sanity/main.nf b/src/nf_modules/sanity/main.nf
index 7d9d6236c94230a845abf688699f268e5dff24ef..53ce03cda4ee3512037f316a97993947e135abd7 100644
--- a/src/nf_modules/sanity/main.nf
+++ b/src/nf_modules/sanity/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
container_url="mlepetit/sanity:latest"
params.sanity_out=""
diff --git a/src/nf_modules/sratoolkit/list-srr.txt.license b/src/nf_modules/sratoolkit/list-srr.txt.license
new file mode 100644
index 0000000000000000000000000000000000000000..f3cd5737c6565583eaceac8a5c2c7aebc6f003fb
--- /dev/null
+++ b/src/nf_modules/sratoolkit/list-srr.txt.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
diff --git a/src/nf_modules/sratoolkit/main.nf b/src/nf_modules/sratoolkit/main.nf
index adca8d41b775493f6633059934d5bd23ff38bbc1..b8dfb7b93d81ddba8ad21dda937b3ae2f73189d2 100644
--- a/src/nf_modules/sratoolkit/main.nf
+++ b/src/nf_modules/sratoolkit/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "3.0.0"
container_url = "lbmc/sratoolkit:${version}"
diff --git a/src/nf_modules/star/main.nf b/src/nf_modules/star/main.nf
index fe62a22ccc2282e6ad57203a3ef195663c86fb76..c8135caa8ac55f78b68ca41e6f980941bf91036a 100644
--- a/src/nf_modules/star/main.nf
+++ b/src/nf_modules/star/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
// STAR is an ultrafast universal RNA-seq aligner
//
// EXAMPLE:
diff --git a/src/nf_modules/stringtie2/main.nf b/src/nf_modules/stringtie2/main.nf
index 04a9b2cf0481b1f30bc6a9c1c7e04f3429dcfd36..5141c1607be6a296e5cd18ca2fcf0dbc1bcb20ba 100644
--- a/src/nf_modules/stringtie2/main.nf
+++ b/src/nf_modules/stringtie2/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.1.1"
container_url = "lbmc/stringtie2:${version}"
diff --git a/src/nf_modules/trinity/main.nf b/src/nf_modules/trinity/main.nf
index e10a79bee30e5a0ee91095c3d7bc3b4ea2bcdbe5..56bf7ad6686713bfcbfc79701c546dd9b4b615be 100644
--- a/src/nf_modules/trinity/main.nf
+++ b/src/nf_modules/trinity/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "2.13.2"
container_url = "lbmc/trinity:${version}"
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index e661e8a559075a163612c21d9d3c8e5777da102e..8ad259f48134f80a96b27594f981297111b270c9 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "407"
container_url = "lbmc/ucsc:${version}"
diff --git a/src/nf_modules/urqt/main.nf b/src/nf_modules/urqt/main.nf
index b91afb74ccad107e7accd76ead32ea9945dda8b1..7a8e56aa14eee0d7d38c3c596de0144c49f97e8f 100644
--- a/src/nf_modules/urqt/main.nf
+++ b/src/nf_modules/urqt/main.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
version = "d62c1f8"
container_url = "lbmc/urqt:${version}"
diff --git a/src/solution_RNASeq.nf b/src/solution_RNASeq.nf
index 23adf0998d2c6d2dfc60697ab140b8b0ebb16ba0..fdcbd87c7567833576706885d7efe67202c41dc2 100644
--- a/src/solution_RNASeq.nf
+++ b/src/solution_RNASeq.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
nextflow.enable.dsl=2
include { fastp } from "./nf_modules/fastp/main.nf"
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 734a7410c3f3d2425a98b2f1462faee929dc68e1..be62887e1ed044aadaf12003860184ca1374734e 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
profiles {
docker {
docker.temp = "auto"
diff --git a/src/training_dataset.nf b/src/training_dataset.nf
index c6f48e882a82eaa7437a409c7500c7045224893e..88b2a2eb9b7cbf8091d42a201a61e80a725812ef 100644
--- a/src/training_dataset.nf
+++ b/src/training_dataset.nf
@@ -1,3 +1,7 @@
+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
/*
small pipeline to build a training dataset from whole genome data