diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index 15844e1082d77f05790453a7113a78bcab5f9f12..ed0c57ba53032e440836f8d79d681f09db9ce10b 100644
--- a/CLIP/iCLIP.snakefile
+++ b/CLIP/iCLIP.snakefile
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 Snakefile to process iCLIP data.
 """
diff --git a/CLIP/iCLIP_trim_and_dedup.sh b/CLIP/iCLIP_trim_and_dedup.sh
index 9acbe2049ce4121164fcf5d837c519be310a2572..73d2dd0d6020a13a5f707806023125a059e7d56c 100755
--- a/CLIP/iCLIP_trim_and_dedup.sh
+++ b/CLIP/iCLIP_trim_and_dedup.sh
@@ -1,5 +1,19 @@
 #!/usr/bin/env bash
 # Usage: iCLIP_trim_and_dedup.sh <trimmer> <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <trimmed_nodedup> <trimmer log> <nb_raw> <nb_adapt> <nb_adapt_deduped> <nb_noadapt> <nb_noadapt_deduped>
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 # http://linuxcommand.org/wss0150.php
 PROGNAME=$(basename $0)
diff --git a/COPYING b/COPYING
index 8d4592e40870c4ef976038efdadf93c60ee1e7de..05aed68ac1f6afb3247f71a079f08cfe415a451f 120000
--- a/COPYING
+++ b/COPYING
@@ -1 +1 @@
-gpl.txt
\ No newline at end of file
+COPYING.txt
\ No newline at end of file
diff --git a/gpl.txt b/COPYING.txt
similarity index 100%
rename from gpl.txt
rename to COPYING.txt
diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index 252b072ddbdc00fcec3952f256ce4b3450b63f10..d62c28f3d65ef1869af0a10ae92eb366e5c9eead 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 Snakefile to analyse Degradome-seq data.
 """
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 8a8cbf33afed23ccbb609374d1650c8221b2a55e..b0fa224af9f9dd69b07e63511c1f9f4972eb7f78 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 Snakefile to analyse PRO-seq data.
 """
diff --git a/PRO-seq/PRO-seq_trim_and_dedup.sh b/PRO-seq/PRO-seq_trim_and_dedup.sh
index 2721816f7e8feb5f690cfc99b5c9ffd772cf0bb6..1b917f8123cf26c78beb3e6ba4ef15ce6ff112a8 100755
--- a/PRO-seq/PRO-seq_trim_and_dedup.sh
+++ b/PRO-seq/PRO-seq_trim_and_dedup.sh
@@ -1,5 +1,19 @@
 #!/usr/bin/env bash
 # Usage: PRO-seq_trim_and_dedup.sh <trimmer> <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <trimmer log> <nb_raw> <nb_adapt> <nb_adapt_deduped> <nb_noadapt> <nb_noadapt_deduped>
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 # http://linuxcommand.org/wss0150.php
 PROGNAME=$(basename $0)
diff --git a/PRO-seq/PRO-seq_trim_only.sh b/PRO-seq/PRO-seq_trim_only.sh
index d887ffef39fc7560d58e432e341df20a80fff6d2..5eba4ed31d0e420f85a25b2ff272547d02722f97 100755
--- a/PRO-seq/PRO-seq_trim_only.sh
+++ b/PRO-seq/PRO-seq_trim_only.sh
@@ -1,5 +1,19 @@
 #!/usr/bin/env bash
 # Usage: PRO-seq_trim_only.sh <trimmer> <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <trimmer log> <nb_raw> <nb_adapt> <nb_noadapt>
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 # http://linuxcommand.org/wss0150.php
 PROGNAME=$(basename $0)
diff --git a/PRO-seq/plot_last_base.R b/PRO-seq/plot_last_base.R
index d76b21b444527e3e633641bd0cff477dad4ee8c1..00f0dd4ef744249e414c99e46c2ccd053bf34dde 100755
--- a/PRO-seq/plot_last_base.R
+++ b/PRO-seq/plot_last_base.R
@@ -1,4 +1,18 @@
 #!/usr/bin/env Rscript
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 options(show.error.locations=TRUE)
 
 # Trying to automatically install docopt
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 67b235dd34066afa3494cc1bc1da94a8e2db18f9..3fce964f8750eac2c50bf11034e317b864f7e7ae 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 Snakefile to analyse RNA-seq data.
 """
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index fb409cdaec27ad27639d9497fcfb06b9322c65ef..95631b073a6586d59367fcb0e43176e444b3cc05 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 Snakefile to analyse small_RNA-seq data.
 
diff --git a/bam25prime b/bam25prime
index b54d1ca837f41e1b8eaf1b7984d4799ca2cc50e4..508be30bc5d719779ad47c0ecc5af06ac890b6df 160000
--- a/bam25prime
+++ b/bam25prime
@@ -1 +1 @@
-Subproject commit b54d1ca837f41e1b8eaf1b7984d4799ca2cc50e4
+Subproject commit 508be30bc5d719779ad47c0ecc5af06ac890b6df
diff --git a/libcelegans b/libcelegans
index 36938bcfd6c1e4d1b51ec39d7706fb17e08a64d4..48afc688faabfee8a9b5ee75b183d93cb8238e12 160000
--- a/libcelegans
+++ b/libcelegans
@@ -1 +1 @@
-Subproject commit 36938bcfd6c1e4d1b51ec39d7706fb17e08a64d4
+Subproject commit 48afc688faabfee8a9b5ee75b183d93cb8238e12
diff --git a/libdeseq b/libdeseq
index c4928c62ba6875dbe83e77caceb7265a7a81045d..196ee3d15a125fad0d821256cc69f96c9129bf61 160000
--- a/libdeseq
+++ b/libdeseq
@@ -1 +1 @@
-Subproject commit c4928c62ba6875dbe83e77caceb7265a7a81045d
+Subproject commit 196ee3d15a125fad0d821256cc69f96c9129bf61
diff --git a/libhts b/libhts
index c4715fde8bf617a87906d9349432b2beb9462a43..4441fea365110ca842eaea5fc5ae69a26765896e 160000
--- a/libhts
+++ b/libhts
@@ -1 +1 @@
-Subproject commit c4715fde8bf617a87906d9349432b2beb9462a43
+Subproject commit 4441fea365110ca842eaea5fc5ae69a26765896e
diff --git a/libsmallrna b/libsmallrna
index 89178795d9dd148b1780a490b70c705b58a64b12..b44e5256fd5d42a63c8f0a6765e0d6af829d753d 160000
--- a/libsmallrna
+++ b/libsmallrna
@@ -1 +1 @@
-Subproject commit 89178795d9dd148b1780a490b70c705b58a64b12
+Subproject commit b44e5256fd5d42a63c8f0a6765e0d6af829d753d
diff --git a/libworkflows b/libworkflows
index 4b3859c4c852c518b18d809954b60d8ce00c5d15..f38327c25d197c04da485d8691a463f10bc10fd4 160000
--- a/libworkflows
+++ b/libworkflows
@@ -1 +1 @@
-Subproject commit 4b3859c4c852c518b18d809954b60d8ce00c5d15
+Subproject commit f38327c25d197c04da485d8691a463f10bc10fd4
diff --git a/plotting_scripts b/plotting_scripts
index 6a7e11405991a4fb273f40e03c5b7c02d1d52faa..03c60f765ee1c9694b93638bae2293539e2cd3c5 160000
--- a/plotting_scripts
+++ b/plotting_scripts
@@ -1 +1 @@
-Subproject commit 6a7e11405991a4fb273f40e03c5b7c02d1d52faa
+Subproject commit 03c60f765ee1c9694b93638bae2293539e2cd3c5
diff --git a/singularity/run_pipeline.def b/singularity/run_pipeline.def
index 2227ac33eddde018a87ca264f86762b52104ba74..c3a287172b0bb5a914152d63f5aac7e6738acc16 100644
--- a/singularity/run_pipeline.def
+++ b/singularity/run_pipeline.def
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 Bootstrap:localimage
 From:workflows_base.sif
 
@@ -37,6 +51,9 @@ From:workflows_base.sif
 	    "--version" | "-v")
 	        exec cat /usr/local/share/doc/program_versions.txt
 	        ;;
+	    "--licence")
+	        exec cat /usr/local/src/bioinfo_utils/COPYING.txt
+	        ;;
 	    "--help" | "-h")
 	        exec echo "Usage: run_<seq_type>_pipeline <config.yaml> [<snakemake options> ...]"
 	        ;;
diff --git a/singularity/workflows_base.def b/singularity/workflows_base.def
index 9327a885ebbcc435efe1abb858a199cecf7cd834..9406e0fe5a35c3ebb646f14bdef76967ad027df2 100644
--- a/singularity/workflows_base.def
+++ b/singularity/workflows_base.def
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 Bootstrap:docker
 From:debian:buster-slim
 Stage: build-haskell
@@ -95,6 +109,7 @@ From:python:3.7-buster
 	prog="bedGraphToBigWig"
 	echo "# ${prog}" >> /usr/local/share/doc/program_versions.txt
 	# `|| :` is to "ignore" error exit code from bedGraphToBigWig
+	# TODO: fix this
 	eval "${prog}" 2>&1 | head -1 >> /usr/local/share/doc/program_versions.txt || :
 	# It is possible to test whether the R install is already OK
 	deb_source="deb http://cran.irsn.fr/bin/linux/debian buster-cran35/"
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index f0187d9513059b57f4f7147593dce1e08fd041de..1e932661a1164acb2da897530fd590e2e7318d92 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -1,3 +1,17 @@
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
 Snakefile to analyse small_RNA-seq data.
 
diff --git a/small_RNA-seq/small_RNA-seq_trim_and_dedup.sh b/small_RNA-seq/small_RNA-seq_trim_and_dedup.sh
index 5a861a5286fe747849f8aaeada23c44a9a86dc48..04058916bc9aca301d3743a02e74005145b82dd9 100755
--- a/small_RNA-seq/small_RNA-seq_trim_and_dedup.sh
+++ b/small_RNA-seq/small_RNA-seq_trim_and_dedup.sh
@@ -1,5 +1,20 @@
 #!/usr/bin/env bash
 # Usage: PRO-seq_trim_and_dedup.sh <raw fastq> <ADAPTER> <trimmed fastq> <untrimmed fastq>
+#
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 # http://linuxcommand.org/wss0150.php
 PROGNAME=$(basename $0)
diff --git a/small_RNA-seq/small_RNA_seq_annotate.py b/small_RNA-seq/small_RNA_seq_annotate.py
index 050c2d1f4383e5eb66781393441bda3d1806d5bd..c6b518118dcc2b304211192cbe4839c341681954 100755
--- a/small_RNA-seq/small_RNA_seq_annotate.py
+++ b/small_RNA-seq/small_RNA_seq_annotate.py
@@ -1,5 +1,18 @@
 #!/usr/bin/env python3
-# vim: set fileencoding=<utf-8> :
+# Copyright (C) 2020 Blaise Li
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """This script parses a sorted bam file and uses annotations from a gtf file to
 identify small RNA categories."""
 
diff --git a/snakemake_wrappers b/snakemake_wrappers
index 1e96ee88d41b9fdc7c15157d15041cbfe34fbc44..c79a4cb434550adcd6cbd1122220f8a32a5744fa 160000
--- a/snakemake_wrappers
+++ b/snakemake_wrappers
@@ -1 +1 @@
-Subproject commit 1e96ee88d41b9fdc7c15157d15041cbfe34fbc44
+Subproject commit c79a4cb434550adcd6cbd1122220f8a32a5744fa