.gitignore

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 nextflow
 .nextflow.log*
 .nextflow/

.gitmodules

+# 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

.reuse/dep5

+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: ...

CHANGELOG.md

+<!--
+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.
 

CONTRIBUTING.md

+<!--
+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,
@@ -139,7 +145,7 @@ If you want to use information within the `file_id` to name outputs in your `scr
       file_prefix = file_id.values()[0]
     break
     default:
-      file_id
+      file_prefix = file_id
     break
   }
 ```

LICENSES/CC-BY-SA-4.0.txt

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+
+Creative Commons may be contacted at creativecommons.org.

README.md

+<!--
+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.
@@ -9,7 +15,7 @@ To get the last commits from this repository into your fork use the following co
 
 For the first time:
 ```sh
-git remote add upstream git@gitbio.ens-lyon.fr::pipelines/nextflow.git
+git remote add upstream git@gitbio.ens-lyon.fr:LBMC/nextflow.git
 git pull upstream master
 ```
 

bin/.gitignore

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 *

data/.gitignore

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 *

doc/.gitignore

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 *.pdf

doc/building_your_pipeline.md

+<!--
+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:
@@ -57,10 +63,10 @@ Here is an example of **process**:
 ```Groovy
 process sample_fasta {
   input:
-  file fasta
+  path fasta
 
   output:
-  file "sample.fasta", emit: fasta_sample
+  path "sample.fasta", emit: fasta_sample
 
   script:
 """
@@ -69,20 +75,20 @@ head ${fasta} > sample.fasta
 }
 ```
 
-We have the process `sample_fasta` that takes fasta `file` input and as output a fasta `file`. The `process` task itself is defined in the `script:` block and within `"""`.
+We have the process `sample_fasta` that takes fasta `path` input and as output a fasta `path`. The `process` task itself is defined in the `script:` block and within `"""`.
 
 ```Groovy
 input:
-file fasta
+path fasta
 ```
 
-When we zoom on the `input:` block, we see that we define a variable `fasta` of type `file`.
+When we zoom on the `input:` block, we see that we define a variable `fasta` of type `path`.
 This means that the `sample_fasta` `process` is going to get a flux of fasta file(s).
 Nextflow is going to write a file named as the content of the variable `fasta` in the root of the folder where `script:` is executed.
 
 ```Groovy
 output:
-file "sample.fasta", emit: fasta_sample
+path "sample.fasta", emit: fasta_sample
 ```
 
 At the end of the script, a file named `sample.fasta` is found in the root the folder where `script:` is executed and will be emitted as `fasta_sample`.
@@ -201,7 +207,7 @@ Every `fasta_sampler` process write a `sample.fasta` file. We need to make the n
 
 ```Groovy
 output:
-file "*_sample.fasta", emit: fasta_sample
+path "*_sample.fasta", emit: fasta_sample
 
   script:
 """
@@ -360,7 +366,7 @@ We can add the `fastq_from_bed` step to our `workflow`
 
 ```Groovy
 workflow {
-  sample_fasta(fasta_file)
+  fastp(fastq_files)
   fasta_from_bed(fasta_files, bed_files)
 }
 ```
@@ -437,7 +443,7 @@ login@allo-psmn
 Then once connected to `allo-psmn`, you can connect to `e5-2667v4comp1`:
 
 ```sh
-login@e5-2667v4comp1
+login@m6142comp2
 ```
 
 ## Set your environment

doc/getting_started.md

+<!--
+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.
@@ -34,7 +40,7 @@ singularity run docker://hello-world
 To install nextflow on your computer simply run the following command:
 
 ```sh
-git clone git@gitbio.ens-lyon.fr/LBMC/nextflow
+git clone git@gitbio.ens-lyon.fr:LBMC/nextflow.git
 cd nextflow/
 src/install_nextflow.sh
 ```
@@ -42,6 +48,7 @@ src/install_nextflow.sh
 ## Running a toy RNASeq quantification pipeline
 
 To run tests we first need to get a training set
+
 ```sh
 cd data
 git clone https://gitbio.ens-lyon.fr/LBMC/Hub/tiny_dataset.git
@@ -63,14 +70,21 @@ By default le `src/nextflow.config` file define 4 different profiles
 
 - `-profile docker` each process of the pipeline will be executed within a `docker` container locally
 - `-profile singularity` each process of the pipeline will be executed within a `singularity` container locally
-- `-profile psmn` each process will be sent as a separate job within a `singularity` container on the PSMN
+- `-profile psmn` each process will be sent as a separate job within a `charliecloud` container on the PSMN
 - `-profile ccin2p3` each process will be sent as a separate job within a `singularity` container on the CCIN2P3
 
-If the containers are not found locally, they are automatically downloaded before running the process. For the PSMN and CCIN2P3, the `singularity` images are downloaded in a shared folder (`/scratch/Bio/singularity` for the PSMN, and `/sps/lbmc/common/singularity/` for the CCIN2P3)
-
+If the containers are not found locally, they are automatically downloaded before running the process. For the PSMN and CCIN2P3, the `singularity` images are downloaded in a shared folder (`/scratch/Bio/charliecloud` for the PSMN, and `/sps/lbmc/common/singularity/` for the CCIN2P3)
 
 ### PSMN
 
+To have access to `charliecloud` on the PSMN you need to add the followin path to your `PATH` variable:
+
+```sh
+PATH=/Xnfs/abc/charliecloud_bin/:$PATH
+```
+
+You can add this line in your `~/.bashrc` or `~/.zshrc` file
+
 When running `nextflow` on the PSMN, we recommend to use `tmux` before launching the pipeline:
 
 ```sh
@@ -83,10 +97,9 @@ You can re-attach the `tmux` session, with the command `tmux a` (and press `ctrl
 
 ### CCIN2P3
 
-When runnning `nextflow` on the CCIN2P3, you cannot use `tmux`, instead you should send a *daemon* jobs which will launch the `nextflow` command.
+When runnning `nextflow` on the CCIN2P3, you cannot use `tmux`, instead you should send a _daemon_ jobs which will launch the `nextflow` command.
 You can edit the `src/ccin2p3.pbs` file to personalize your `nextflow` command and send it with the command:
 
 ```sh
 qsub src/ccin2p3.pbs
 ```
-

doc/img/fork.png.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

doc/img/merge_request.png.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

doc/img/webide.png.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

doc/mail.txt.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

doc/nf_projects.md

+<!--
+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
@@ -15,7 +21,8 @@ To add your project to this list, please fork this project, modify this file and
 - [https://_https://gitlab.biologie.ens-lyon.fr/gylab/salmoninyeast](https://_https://gitlab.biologie.ens-lyon.fr/gylab/salmoninyeast)
 - [https://github.com/LBMC/readthroughpombe](https://github.com/LBMC/readthroughpombe)
 - [https://_https://gitlab.biologie.ens-lyon.fr/vvanoost/nextflow](https://_https://gitlab.biologie.ens-lyon.fr/vvanoost/nextflow)
-- [https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project](https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project)
+- [https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project](https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project)  
+- [https://gitbio.ens-lyon.fr/LBMC/Palladino/RNAseq_nextflow](https://gitbio.ens-lyon.fr/LBMC/Palladino/RNAseq_nextflow)
 
 ### scRNASeq