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

+[Formation BioComp] nextflow for experimental biologists
+
+Dear all,
+
+You registered for the nextflow formation which will take place this  afternoon starting at 13h30 in the room M7.1H04.
+
+Please check that you have an account on our gitlab server at the following url : 
+https://gitlab.biologie.ens-lyon.fr
+To connect, simply click on the CAS button.
+Your account is now linked to the gitlab server, but blocked
+You can send an email to laurent.modolo@ens-lyon.fr to activate your account.
+
+You will also need an account on the PSMN (http://www.ens-lyon.fr/PSMN/doku.php?id=contact:forms:inscription)
+
+If you want to work on your laptop, or plan to work remotely on your desktop via ssh (http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/bioinfo_club/1_ssh_and_other_tools_to_work_remotly) you need to have the following software installed :
+- ssh
+- git
+- java (>=1.8)
+- docker
+
+Best,
+
+Dear all,
+
+You registered to the formation Git (12/12) or/and the formation Nextlflow (13/12) from 13:30 pm to 18pm in the in the room M7.1H04.
+
+Please check that you have an account on our gitlab server at the following url : 
+https://gitlab.biologie.ens-lyon.fr (only available from the ENS network)
+To connect, simply click on the CAS button.
+Your account is now linked to the gitlab server, but blocked
+You can send an email to laurent.modolo@ens-lyon.fr to activate your account.
+
+You will also need an account on the PSMN (http://www.ens-lyon.fr/PSMN/doku.php?id=contact:forms:inscription) (don’t wait until the 12 to request an account !)
+
+If you want to work on your laptop, or plan to work remotely on your desktop via ssh (http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/bioinfo_club/1_ssh_and_other_tools_to_work_remotly) you need to have the following software installed :
+- ssh
+- git
+- java (>=1.8) (for the nextflow formation)
+- docker (for the nextflow formation)
+Otherwise, you will need to request an account to use the computer in the room (http://www.cbp.ens-lyon.fr/doku.php?id=contact:compte)
+
+Best,

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
+
+- [RNASeq](./nf_projects.md#rnaseq)
+- [scRNASeq](./nf_projects.m#scrnaseq)
+- [DNASeq](./nf_projects.md#dnaseq)
+- [ChipSeq](./nf_projects.md#chipseq)
+
+To add your project to this list, please fork this project, modify this file and make a merge request.
+![merge request button](./img/merge_request.png)
+
+### RNASeq
+
+- [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://gitbio.ens-lyon.fr/LBMC/Palladino/RNAseq_nextflow](https://gitbio.ens-lyon.fr/LBMC/Palladino/RNAseq_nextflow)
+
+### scRNASeq
+
+- [https://gitlab.com/LBMC_UMR5239/sbdm/mars-seq](https://gitlab.com/LBMC_UMR5239/sbdm/mars-seq)
+
+### DNASeq
+
+- [https://github.com/LBMC/ChrSexebelari](https://github.com/LBMC/ChrSexebelari)
+- [https://gitbio.ens-lyon.fr/LBMC/gylab/MappingNoise](https://gitbio.ens-lyon.fr/LBMC/gylab/MappingNoise)
+- [https://gitbio.ens-lyon.fr/LBMC/qrg/droso_hic_group/droso_haplo_rna_seq](https://gitbio.ens-lyon.fr/LBMC/qrg/droso_hic_group/droso_haplo_rna_seq)
+
+### Chip-Seq
+
+- [https://gitlab.biologie.ens-lyon.fr/Auboeuf/ChIP-seq](https://gitlab.biologie.ens-lyon.fr/Auboeuf/ChIP-seq)
+- [https://gitbio.ens-lyon.fr/LBMC/Bernard/quantitative-nucleosome-analysis](https://gitbio.ens-lyon.fr/LBMC/Bernard/quantitative-nucleosome-analysis)
+

results/.gitignore

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

src/.docker_modules/CITE-seq-Count/1.4.5/Dockerfile

+# 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
+ENV PACKAGES procps locales gcc libstdc++-10-dev libcurl4 libc6 python3 python3-pip python3-dev
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install CITE-seq-Count==${CITESEQ_VERSION}
+

src/.docker_modules/CITE-seq-Count/1.4.5/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/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
+# docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/cite_seq_count:1.4.5" --push src/.docker_modules/CITE-seq-Count/1.4.5

src/.docker_modules/CITE-seq-Count/1.5.0/Dockerfile

+# 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
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+RUN git clone https://github.com/Hoohm/CITE-seq-Count.git \
+    && cd CITE-seq-Count \
+    && git checkout 1.5.0-alpha \
+    && pip3 install requests pooch \
+    && pip3 install ./
+

src/.docker_modules/CITE-seq-Count/1.5.0/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/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
+# docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/cite_seq_count:1.5.0" --push src/.docker_modules/CITE-seq-Count/1.5.0

src/.docker_modules/agat/0.8.0/Dockerfile

+# 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

src/.docker_modules/agat/0.8.0/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/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
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/agat:0.8.0" --push src/.docker_modules/agat/0.8.0

src/.docker_modules/alntools/dd96682/Dockerfile

+# 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
+
+ENV ALNTOOLS_VERSION=dd96682
+ENV PACKAGES git \
+    ca-certificates \
+    gawk \
+    procps
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends ${PACKAGES}\
+    && apt-get clean \
+    && git clone https://github.com/churchill-lab/alntools.git \
+    && cd alntools \
+    && git checkout ${ALNTOOLS_VERSION} \
+    && python setup.py install \
+    && cd .. \
+    && rm -R alntools \
+    && pip install six \
+    && apt-get autoremove --purge -y git ca-certificates
+
+CMD ["bash"] 
\ No newline at end of file

src/.docker_modules/alntools/dd96682/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/alntools:dd96682
+# docker build src/.docker_modules/alntools/dd96682 -t 'lbmc/alntools:dd96682'
+# docker push lbmc/alntools:dd96682
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/alntools:dd96682" --push src/.docker_modules/alntools/dd96682

src/.docker_modules/bamutils/1.0.14/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
+
+ENV BAMUTILS_VERSION=1.0.14
+ENV PACKAGES git \
+             build-essential \
+             g++ \
+             libssl-dev \
+             zlib1g-dev
+
+RUN apt-get update && apt-get -y install  ${PACKAGES}
+
+RUN git clone https://github.com/statgen/libStatGen && \
+cd libStatGen && \
+git checkout fae4fca874b3b78bf9b61c0 && \
+make && \
+cd ../ && \
+git clone https://github.com/statgen/bamUtil && \
+cd bamUtil && \
+git checkout v${BAMUTILS_VERSION} && \
+make && \
+make install

src/.docker_modules/bamutils/1.0.14/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/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
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bamutils:1.0.14" --push src/.docker_modules/bamutils/1.0.14

src/docker_modules/SAMtools/1.7/Dockerfile → src/.docker_modules/bcftools/1.7/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
 
-ENV SAMTOOLS_VERSION=1.7
-ENV PACKAGES samtools=${SAMTOOLS_VERSION}*
+ENV BCFTOOLS_VERSION=1.7
+ENV PACKAGES bcftools=${BCFTOOLS_VERSION}*
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \

src/.docker_modules/bcftools/1.7/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/bcftools:1.7
+# docker build src/.docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
+# docker push lbmc/bcftools:1.7
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bcftools:1.7" --push src/.docker_modules/bcftools/1.7

src/.docker_modules/bedops/2.4.39/Dockerfile

+# 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

src/.docker_modules/bedops/2.4.39/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/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
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bedops:2.4.39" --push src/.docker_modules/bedops/2.4.39

src/docker_modules/BEDtools/2.25.0/Dockerfile → src/.docker_modules/bedtools/2.25.0/Dockerfile

+# 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