Merge branch 'master' into dev

.gitmodules

-[submodule "src/sge_modules"]
-	path = src/.psmn_modules
-	url = gitlab_lbmc:PSMN/modules.git

CHANGELOG.md

@@ -4,6 +4,19 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.0] - 2019-11-18
+### Added
+- Add new tools (star,...)
+- conda support at the psmn
+
+## Changed
+- configuration simplification
+- docker and singularity image download instead of local build
+- hidden directories in `src` for project clarity (only `nf_modules` is visible)
+
+## Removed
+- conda support at in2p3 with `-profile in2p3_conda`
+
 ## [0.3.0] - 2019-05-23
 ### Added
 - Add new tools (umi_tools, fastp,...)

README.md

@@ -8,7 +8,7 @@ To get the last commits from this repository into your fork use the following co
 git remote add upstream gitlab_lbmc:pipelines/nextflow.git
 git pull upstream master
 ```
-If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).
+**If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).**
 
 ## Getting Started
 

doc/available_tools.md

@@ -34,6 +34,7 @@ sambamba | ok | ok | ok | ok
 samblaster | ok | ok | ok | ok
 SAMtools | ok | ok | ok | ok
 SRAtoolkit | ok | ok | ok | ok
+STAR | ok | ok | ok | ok
 subread | **no** | ok | ok | ok
 TopHat | **no** | ok | ok | ok
 Trimmomatic | **no** | ok | ok | ok

doc/nf_projects.md

@@ -5,6 +5,7 @@
 - [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)
 
 ### single-cell RNA_-Seq
 

src/.conda_packages.sh

@@ -147,3 +147,12 @@ fi
 if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
   conda create --yes --name star_2.7.3a star=2.7.3a
 fi
+if [ ! -d ${CONDA_ENVS}liftover_357 ]; then
+  conda create --yes --name liftover_357 ucsc-liftover==357
+fi
+if [ ! -d ${CONDA_ENVS}axtchain_377 ]; then
+  conda create --yes --name axtchain_377 ucsc-axtchain==377
+fi
+if [ ! -d ${CONDA_ENVS}ribotish_0.2.4 ]; then
+  conda create --name ribotish_0.2.4 ribotish=0.2.4
+fi

src/.docker_modules/bcftools/1.7/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/bcftools/1.7 -t 'lbmc/bcftools:1.7'
+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

src/.docker_modules/bedtools/2.25.0/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/bedtools/2.25.0 -t 'lbmc/bedtools:2.25.0'
+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

src/.docker_modules/bioawk/1.0/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
+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

src/.docker_modules/bowtie/1.2.2/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
+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

src/.docker_modules/bowtie2/2.3.4.1/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
+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

src/.docker_modules/bwa/0.7.17/Dockerfile

-FROM sambamba:0.6.7
+FROM lbmc/sambamba:0.6.9
 MAINTAINER Laurent Modolo
 
 ENV BWA_VERSION=0.7.17
 ENV SAMBLASTER_VERSION=0.1.24
 
-ENV PACKAGES curl=7.58.0* \
+ENV PACKAGES curl=7.58* \
     ca-certificates=20180409 \
     build-essential=12.4* \
     zlib1g-dev=1:1.2.11*

src/.docker_modules/bwa/0.7.17/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
+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

src/.docker_modules/canu/1.6/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
+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

src/.docker_modules/cutadapt/1.14/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
+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

src/.docker_modules/cutadapt/1.15/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
+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

src/.docker_modules/cutadapt/2.1/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
+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

src/.docker_modules/deeptools/3.0.2/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
+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

src/.docker_modules/deeptools/3.1.1/docker_init.sh

 #!/bin/sh
-docker build src/docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
+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

src/.docker_modules/docker_push.sh

 #!/bin/sh
-fd "Dockerfile" src/docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'
+fd "Dockerfile" src/.docker_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'