src/.docker_modules/trimmomatic/0.36/docker_init.sh

 #!/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

src/.docker_modules/trinity/2.13.2/Dockerfile

+# 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

src/.docker_modules/trinity/2.13.2/docker_init.sh

+#!/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
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/trinity:2.13.2" --push src/.docker_modules/trinity/2.13.2

src/.docker_modules/ucsc/375/Dockerfile

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

src/.docker_modules/ucsc/375/docker_init.sh

 #!/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

src/.docker_modules/ucsc/400/Dockerfile

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

src/.docker_modules/ucsc/400/docker_init.sh

 #!/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

src/.docker_modules/ucsc/407/Dockerfile

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

src/.docker_modules/ucsc/407/bedgraph_to_wig.pl

 #!/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). 

src/.docker_modules/ucsc/407/docker_init.sh

 #!/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

src/.docker_modules/ucsc/407/gtf2bed.pl

 #!/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;
 

src/.docker_modules/umi_tools/0.5.4/Dockerfile

+# 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

src/.docker_modules/umi_tools/0.5.4/docker_init.sh

 #!/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

src/.docker_modules/umi_tools/1.0.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM debian:stretch
 MAINTAINER Rémi SERAPHIN
 

src/.docker_modules/umi_tools/1.0.0/docker_init.sh

 #!/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

src/.docker_modules/urqt/d62c1f8/Dockerfile

+# 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
 

src/.docker_modules/urqt/d62c1f8/docker_init.sh

 #!/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

src/example_chipseq.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
 
 nextflow.enable.dsl=2
 

src/example_marseq.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 nextflow.enable.dsl=2
 
 /*

src/example_variant_calling.nf

+// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+//
+// SPDX-License-Identifier: AGPL-3.0-or-later
+
 nextflow.enable.dsl=2
 
 /*