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Unverified Commit 11a00225 authored by Laurent Modolo's avatar Laurent Modolo
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Merge remote-tracking branch 'origin/master'

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README.md
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......@@ -5,7 +5,7 @@ You can fork this repository to build your own pipeline.
To get the last commits from this repository into your fork use the following commands:
```sh
git remote add upstream gitlab_lbmc:pipelines/nextflow.git
git remote add upstream git@gitbio.ens-lyon.fr::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).**
......
doc/TP_experimental_biologists.md
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......@@ -143,7 +143,7 @@ We also need data to run our pipeline:
```
cd data
git clone git@gitbio.ens-lyon.fr:LBMC/tiny_dataset.git
git clone git@gitbio.ens-lyon.fr:LBMC/hub/tiny_dataset.git
cd ..
```
......@@ -352,7 +352,7 @@ Then you need to clone your pipeline and get the data:
git config --global http.sslVerify false
git clone https://gitbio.ens-lyon.fr/<usr_name>/nextflow.git
cd nextflow/data
git clone https://gitbio.ens-lyon.fr/LBMC/tiny_dataset.git
git clone https://gitbio.ens-lyon.fr/LBMC/hub/tiny_dataset.git
git config --global http.sslVerify true
cd ..
```
......
src/.docker_modules/bamutils/1.0.14/Dockerfile 0 → 100644
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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 0 → 100755
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#!/bin/sh
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
src/.docker_modules/freebayes/1.3.2/Dockerfile 0 → 100644
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FROM quay.io/biocontainers/freebayes:1.3.2--py36h89e4507_1
MAINTAINER Laurent Modolo
src/.docker_modules/freebayes/1.3.2/docker_init.sh 0 → 100755
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#!/bin/sh
docker pull lbmc/freebayes:1.3.2
docker build src/.docker_modules/freebayes/1.3.2/ -t 'lbmc/freebayes:1.3.2'
docker push lbmc/freebayes:1.3.2
src/nf_modules/cutadapt/adaptor_removal_paired.config
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......@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -25,7 +25,7 @@ profiles {
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......@@ -41,7 +41,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
......
src/nf_modules/cutadapt/adaptor_removal_single.config
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......@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -25,7 +25,7 @@ profiles {
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......@@ -41,7 +41,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
......
src/nf_modules/cutadapt/trimming_paired.config
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......@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -25,7 +25,7 @@ profiles {
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......@@ -41,7 +41,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
......
src/nf_modules/cutadapt/trimming_single.config
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......@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -14,7 +14,7 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
......@@ -25,7 +25,7 @@ profiles {
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
......@@ -41,7 +41,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
container = "lbmc/cutadapt:2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
......
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