diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..199db4809ba27cae7eec980d541dc138b7e8e229
--- /dev/null
+++ b/README.md
@@ -0,0 +1,43 @@
+# nextflow pipeline
+
+This repository is a template and a library repository to help you build nextflow pipeline.
+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 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).**
+
+## Getting Started
+
+These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
+
+[you can follow them here.](doc/getting_started.md)
+
+## Available tools
+
+[The list of available tools.](doc/available_tools.md)
+
+## Projects using nextflow
+
+[A list of projects using nextflow at the LBMC.](doc/nf_projects.md)
+
+## Contributing
+
+Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.
+
+## Versioning
+
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitbio.ens-lyon.fr/pipelines/nextflow/tags).
+
+## Authors
+
+* **Laurent Modolo** - *Initial work*
+
+See also the list of [contributors](https://gitbio.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.
+
+## License
+
+This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details
diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md
index 03e9928a386f2ff64a6ee8a753c523592c8f05b5..ed222a3c0a3a6dc39c90808a69e5515c4a46e95e 100644
--- a/doc/TP_experimental_biologists.md
+++ b/doc/TP_experimental_biologists.md
@@ -25,12 +25,12 @@ You are going to build a pipeline for you or your team. So the first step is to
## Forking
-Instead of reinventing the wheel, you can use the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) as a template.
-To easily do so, go to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) repository and click on the [**fork**](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/forks/new) button (you need to log-in).
+Instead of reinventing the wheel, you can use the [LBMC/nextflow](https://gitbio.ens-lyon.fr/LBMC/nextflow) as a template.
+To easily do so, go to the [LBMC/nextflow](https://gitbio.ens-lyon.fr/LBMC/nextflow) repository and click on the [**fork**](https://gitbio.ens-lyon.fr/LBMC/nextflow/forks/new) button (you need to log-in).
-In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository create a merge request (here [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow)). Merge requests are sent to the source repository to ask the maintainers to integrate modifications.
+In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository create a merge request (here [LBMC/nextflow](https://gitbio.ens-lyon.fr/LBMC/nextflow)). Merge requests are sent to the source repository to ask the maintainers to integrate modifications.
@@ -38,20 +38,20 @@ In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributi
This project (and yours) follows the [guide of good practices for the LBMC](http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/ressources/good_practice_LBMC)
-You are now on the main page of your fork of the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow). You can explore this project, all the code in it is under the CeCILL licence (in the [LICENCE](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/LICENSE) file).
+You are now on the main page of your fork of the [LBMC/nextflow](https://gitbio.ens-lyon.fr/LBMC/nextflow). You can explore this project, all the code in it is under the CeCILL licence (in the [LICENCE](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/LICENSE) file).
-The [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md) file contains instructions to run your pipeline and test its installation.
+The [README.md](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/README.md) file contains instructions to run your pipeline and test its installation.
-The [CONTRIBUTING.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/CONTRIBUTING.md) file contains guidelines if you want to contribute to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) (making a merge request for example).
+The [CONTRIBUTING.md](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/CONTRIBUTING.md) file contains guidelines if you want to contribute to the [LBMC/nextflow](https://gitbio.ens-lyon.fr/LBMC/nextflow) (making a merge request for example).
-The [data](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/data) folder will be the place where you store the raw data for your analysis.
-The [results](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/results) folder will be the place where you store the results of your analysis.
+The [data](https://gitbio.ens-lyon.fr/LBMC/nextflow/tree/master/data) folder will be the place where you store the raw data for your analysis.
+The [results](https://gitbio.ens-lyon.fr/LBMC/nextflow/tree/master/results) folder will be the place where you store the results of your analysis.
> **The content of `data` and `results` folders should never be saved on git.**
-The [doc](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/doc) folder contains the documentation of this practical course.
+The [doc](https://gitbio.ens-lyon.fr/LBMC/nextflow/tree/master/doc) folder contains the documentation of this practical course.
-And most interestingly for you, the [src](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src) contains code to wrap tools. This folder contains one visible subdirectories `nf_modules` some pipeline examples and other hidden files.
+And most interestingly for you, the [src](https://gitbio.ens-lyon.fr/LBMC/nextflow/tree/master/src) contains code to wrap tools. This folder contains one visible subdirectories `nf_modules` some pipeline examples and other hidden files.
### `nf_modules`
@@ -124,7 +124,7 @@ After writing this first pipeline, you may want to test it. To do that, first cl
You can then run the following commands to download your project on your computer:
-If you are on a PSMN computer:
+If you are on a PSMN PC:
```sh
pip install cutadapt=1.14
@@ -134,7 +134,7 @@ PATH="/scratch/lmodolo/:$PATH"
and then :
```sh
-git clone gitlab_lbmc:<usr_name>/nextflow.git
+git clone git@gitbio.ens-lyon.fr:<usr_name>/nextflow.git
cd nextflow
src/install_nextflow.sh
```
@@ -143,7 +143,7 @@ We also need data to run our pipeline:
```
cd data
-git clone gitlab_lbmc:LBMC/tiny_dataset.git
+git clone git@gitbio.ens-lyon.fr:LBMC/hub/tiny_dataset.git
cd ..
```
@@ -210,7 +210,7 @@ In this section you are going to build your own pipeline for RNASeq analysis fro
The first step of the pipeline is to remove any Illumina adaptors left in your read files.
-Open the WebIDE and create a `src/RNASeq.nf` file. Browse for [src/nf_modules/cutadapt/adaptor_removal_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.nf), this file contains examples for cutadapt. We are interested in the *Illumina adaptor removal*, *for paired-end data* section of the code. Copy this code in your pipeline and commit it.
+Open the WebIDE and create a `src/RNASeq.nf` file. Browse for [src/nf_modules/cutadapt/adaptor_removal_paired.nf](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.nf), this file contains examples for cutadapt. We are interested in the *Illumina adaptor removal*, *for paired-end data* section of the code. Copy this code in your pipeline and commit it.
Compared to before, we have few new lines:
@@ -247,7 +247,7 @@ For the `fastq_sampler.nf` pipeline we used the command `head` present in most b
- launch the process in a Docker container that has cutadapt installed
- launch the process with psmn while loading the correct module to have cutadapt available
-We are not going to use the first option which requires no configuration for nextflow but tedious tools installations. Instead, we are going to use existing *wrappers* and tell nextflow about it. This is what the [src/nf_modules/cutadapt/adaptor_removal_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.config) is used for.
+We are not going to use the first option which requires no configuration for nextflow but tedious tools installations. Instead, we are going to use existing *wrappers* and tell nextflow about it. This is what the [src/nf_modules/cutadapt/adaptor_removal_paired.config](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/cutadapt/adaptor_removal_paired.config) is used for.
Copy the content of this config file to an `src/RNASeq.config` file. This file is structured in process blocks. Here we are only interested in configuring `adaptor_removal` process not `trimming` process. So you can remove the `trimming` block and commit it.
@@ -262,7 +262,7 @@ You can test your pipeline with the following command:
The second step of the pipeline is to trim reads by quality.
-Browse for [src/nf_modules/urqt/trimming_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.nf), this file contains examples for UrQt. We are interested in the *for paired-end data* section of the code. Copy the process section code in your pipeline and commit it.
+Browse for [src/nf_modules/urqt/trimming_paired.nf](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.nf), this file contains examples for UrQt. We are interested in the *for paired-end data* section of the code. Copy the process section code in your pipeline and commit it.
This code won’t work if you try to run it: the `fastq_file` channel is already consumed by the `adaptor_removal` process. In nextflow once a channel is used by a process, it ceases to exist. Moreover, we don’t want to trim the input fastq, we want to trim the fastq that comes from the `adaptor_removal` process.
@@ -280,7 +280,7 @@ set pair_id, file(reads) from fastq_files_cut
The two processes are now connected by the channel `fastq_files_cut`.
-Add the content of the [src/nf_modules/urqt/trimming_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.config) file to your `src/RNASeq.config` file and commit it.
+Add the content of the [src/nf_modules/urqt/trimming_paired.config](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/urqt/trimming_paired.config) file to your `src/RNASeq.config` file and commit it.
You can test your pipeline.
@@ -288,7 +288,7 @@ You can test your pipeline.
Kallisto need the sequences of the transcripts that need to be quantified. We are going to extract these sequences from the reference `data/tiny_dataset/fasta/tiny_v2.fasta` with the `bed` annotation `data/tiny_dataset/annot/tiny.bed`.
-You can copy to your `src/RNASeq.nf` file the content of [src/nf_modules/bedtools/fasta_from_bed.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/bedtools/fasta_from_bed.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.config).
+You can copy to your `src/RNASeq.nf` file the content of [src/nf_modules/bedtools/fasta_from_bed.nf](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.nf) and to your `src/RNASeq.config` file the content of [src/nf_modules/bedtools/fasta_from_bed.config](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/bedtools/fasta_from_bed.config).
Commit your work and test your pipeline with the following command:
@@ -300,7 +300,7 @@ Commit your work and test your pipeline with the following command:
Kallisto run in two steps: the indexation of the reference and the quantification on this index.
-You can copy to your `src/RNASeq.nf` file the content of the files [src/nf_modules/kallisto/indexing.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.nf) and [src/nf_modules/kallisto/mapping_paired.nf](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.nf). You can add to your file `src/RNASeq.config` file the content of the files [src/nf_modules/kallisto/indexing.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/indexing.config) and [src/nf_modules/kallisto/mapping_paired.config](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.config).
+You can copy to your `src/RNASeq.nf` file the content of the files [src/nf_modules/kallisto/indexing.nf](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/kallisto/indexing.nf) and [src/nf_modules/kallisto/mapping_paired.nf](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.nf). You can add to your file `src/RNASeq.config` file the content of the files [src/nf_modules/kallisto/indexing.config](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/kallisto/indexing.config) and [src/nf_modules/kallisto/mapping_paired.config](https://gitbio.ens-lyon.fr/LBMC/nextflow/blob/master/src/nf_modules/kallisto/mapping_paired.config).
We are going to work with paired-end so only copy the relevant processes. The `index_fasta` process needs to take as input the output of your `fasta_from_bed` process. The `fastq` input of your `mapping_fastq` process needs to take as input the output of your `index_fasta` process and the `trimming` process.
@@ -350,9 +350,9 @@ Then you need to clone your pipeline and get the data:
```sh
git config --global http.sslVerify false
-git clone https://gitlab.biologie.ens-lyon.fr/<usr_name>/nextflow.git
+git clone https://gitbio.ens-lyon.fr/<usr_name>/nextflow.git
cd nextflow/data
-git clone https://gitlab.biologie.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 ..
```
@@ -363,8 +363,8 @@ As we don’t want nextflow to be killed in case of disconnection, we start by l
```sh
tmux
-module load nextflow/0.28.2
-nextflow src/RNASeq.nf -c src/RNASeq.config -profile psmn --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq" --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -w /scratch/<login>
+src/install_nextflow.sh
+./nextflow src/RNASeq.nf -c src/RNASeq.config -profile psmn --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq" --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -w /scratch/Bio/<login>
```
To use the scratch for nextflow computations add the option :
diff --git a/doc/getting_started.md b/doc/getting_started.md
index e8446e5b9d12a60e9330f4bb40f301f7c17e59b2..b9ef5cee8438dcf7fe59b8931cecbcfb6830cba3 100644
--- a/doc/getting_started.md
+++ b/doc/getting_started.md
@@ -46,7 +46,7 @@ find src/docker_modules/ -name "docker_init.sh" | awk '{system($0)}'
To run tests we first need to get a training set
```sh
cd data
-git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
+git clone https://gitbio.ens-lyon.fr/LBMC/Hub/tiny_dataset.git
cp tiny_dataset/fastq/tiny_R1.fastq tiny_dataset/fastq/tiny2_R1.fastq
cp tiny_dataset/fastq/tiny_R2.fastq tiny_dataset/fastq/tiny2_R2.fastq
cp tiny_dataset/fastq/tiny_S.fastq tiny_dataset/fastq/tiny2_S.fastq
diff --git a/src/.conda_envs/bwa_0.7.17 b/src/.conda_envs/bwa_0.7.17
new file mode 120000
index 0000000000000000000000000000000000000000..8ee9986b6d7c9423cf8ca4254d5e70296813955f
--- /dev/null
+++ b/src/.conda_envs/bwa_0.7.17
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/bwa_0.7.17
\ No newline at end of file
diff --git a/src/.conda_envs/gatk_3.8.0 b/src/.conda_envs/gatk_3.8.0
new file mode 120000
index 0000000000000000000000000000000000000000..0463b9ccef8d7cc0caf0455d9ff9d550e6c31be6
--- /dev/null
+++ b/src/.conda_envs/gatk_3.8.0
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/gatk_3.8.0
\ No newline at end of file
diff --git a/src/.conda_envs/last_1060 b/src/.conda_envs/last_1060
new file mode 120000
index 0000000000000000000000000000000000000000..2015c9856db5613f43e7287649b2508366e7a260
--- /dev/null
+++ b/src/.conda_envs/last_1060
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/envs/last_1060
\ No newline at end of file
diff --git a/src/.conda_packages.sh b/src/.conda_packages.sh
index 909ca4cb6552d1b1da98dde03b210c5fa37bdd98..86b2575c836ccb90a8d554cdbb6819280865ed8e 100644
--- a/src/.conda_packages.sh
+++ b/src/.conda_packages.sh
@@ -45,6 +45,9 @@ fi
if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
fi
+if [ ! -d ${CONDA_ENVS}bwa_0.7.17 ]; then
+ conda create --yes --name bwa_0.7.17 -c bioconda bwa=0.7.17
+fi
if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
fi
diff --git a/src/.docker_modules/bamutils/1.0.14/Dockerfile b/src/.docker_modules/bamutils/1.0.14/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..9a116c6d442d99a997f1d9f5ada95a46e5366ab1
--- /dev/null
+++ b/src/.docker_modules/bamutils/1.0.14/Dockerfile
@@ -0,0 +1,22 @@
+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
diff --git a/src/.docker_modules/bamutils/1.0.14/docker_init.sh b/src/.docker_modules/bamutils/1.0.14/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2d89e9ccd542b1a848d74231068cff94bfe92239
--- /dev/null
+++ b/src/.docker_modules/bamutils/1.0.14/docker_init.sh
@@ -0,0 +1,4 @@
+#!/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
diff --git a/src/.docker_modules/freebayes/1.3.2/Dockerfile b/src/.docker_modules/freebayes/1.3.2/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..f696522d1663186e96949ff9a28f79847f048a77
--- /dev/null
+++ b/src/.docker_modules/freebayes/1.3.2/Dockerfile
@@ -0,0 +1,2 @@
+FROM quay.io/biocontainers/freebayes:1.3.2--py36h89e4507_1
+MAINTAINER Laurent Modolo
diff --git a/src/.docker_modules/freebayes/1.3.2/docker_init.sh b/src/.docker_modules/freebayes/1.3.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3dee0714d779f3df172fb007962dcf5219f7cc3f
--- /dev/null
+++ b/src/.docker_modules/freebayes/1.3.2/docker_init.sh
@@ -0,0 +1,4 @@
+#!/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
diff --git a/src/.docker_modules/gatk/3.8.0/Dockerfile b/src/.docker_modules/gatk/3.8.0/Dockerfile
index 185b9121939870446238396a3b7a1fbc30f7b8cc..af8e30448ea39b16a558d7d4bd8f1fb7ce4b9b2d 100644
--- a/src/.docker_modules/gatk/3.8.0/Dockerfile
+++ b/src/.docker_modules/gatk/3.8.0/Dockerfile
@@ -2,3 +2,7 @@ FROM broadinstitute/gatk3:3.8-0
MAINTAINER Laurent Modolo
ENV GATK_VERSION=3.8.0
+
+RUN echo "#\!/bin/sh\njava -jar /usr/GenomeAnalysisTK.jar \$@" > /bin/gatk3
+RUN chmod +x /bin/gatk3
+RUN sed -i 's/java/java -Xmx128g/g' /bin/gatk3
diff --git a/src/.docker_modules/kallistobustools/0.24.4/Dockerfile b/src/.docker_modules/kallistobustools/0.24.4/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..b3bb53556f54e2e47510dd89d79e273ea2f3723f
--- /dev/null
+++ b/src/.docker_modules/kallistobustools/0.24.4/Dockerfile
@@ -0,0 +1,9 @@
+FROM python:3.7
+MAINTAINER Laurent Modolo
+
+ENV KB_VERSION=0.24.4
+
+RUN pip3 install kb_python==${KB_VERSION}
+ENTRYPOINT ["/bin/sh"]
+RUN ln -s /usr/local/lib/python3.7/site-packages/kb_python/bins/linux/bustools/bustools /usr/local/bin/
+RUN ln -s /usr/local/lib/python3.7/site-packages/kb_python/bins/linux/kallisto/kallisto /usr/local/bin/
diff --git a/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh b/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..216b302fea20598e923a7ab21d492235042f1738
--- /dev/null
+++ b/src/.docker_modules/kallistobustools/0.24.4/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/kallistobustools:0.24.4
+docker build src/.docker_modules/kallistobustools/0.24.4 -t 'lbmc/kallistobustools:0.24.4'
+docker push lbmc/kallistobustools:0.24.4
diff --git a/src/.docker_modules/last/1060/Dockerfile b/src/.docker_modules/last/1060/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..4193a11f30d443b870a188bebffc33c56038d336
--- /dev/null
+++ b/src/.docker_modules/last/1060/Dockerfile
@@ -0,0 +1,25 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV LAST_VERSION=1060
+ENV PACKAGES curl=7.58.0* \
+ unzip \
+ make=4.1* \
+ g++ \
+ zlib1g-dev=1:1.2.11* \
+ ca-certificates=20180409 \
+ build-essential=12.4* \
+ python
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends ${PACKAGES} && \
+ apt-get clean
+
+RUN curl -k -L http://last.cbrc.jp/last-${LAST_VERSION}.zip -o last-${LAST_VERSION}.zip && \
+unzip last-${LAST_VERSION}.zip && \
+cd last-${LAST_VERSION} && \
+make && \
+cp src/last* /usr/bin/ && \
+cp scripts/* /usr/bin/ && \
+cd .. && \
+rm -Rf last-${LAST_VERSION}
diff --git a/src/.docker_modules/last/1060/docker_init.sh b/src/.docker_modules/last/1060/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..0e8393fb88f803e9648cc1185f10c3198daf5976
--- /dev/null
+++ b/src/.docker_modules/last/1060/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/last:1060
+docker build src/.docker_modules/last/1060/ -t 'lbmc/last:1060'
+docker push lbmc/last:1060
diff --git a/src/.docker_modules/picard/2.18.11/PicardCommandLine b/src/.docker_modules/picard/2.18.11/PicardCommandLine
index ce067365785f2f03c722668eff8d80a94b9b34d3..c8eebf8345906cae9ef2e63409500857de479f09 100644
--- a/src/.docker_modules/picard/2.18.11/PicardCommandLine
+++ b/src/.docker_modules/picard/2.18.11/PicardCommandLine
@@ -12,4 +12,4 @@ PicardCommandLine)
;;
esac
-exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
+exec java -Xmx40g ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
diff --git a/src/.docker_modules/r/3.6.2/Dockerfile b/src/.docker_modules/r/3.6.2/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..fd4dcf7867019a2ecb73241fd0d6d39c7196fec1
--- /dev/null
+++ b/src/.docker_modules/r/3.6.2/Dockerfile
@@ -0,0 +1,37 @@
+FROM alpine:3.11.5
+MAINTAINER Lauret Modolo
+
+ENV R_PKGS R=~3.6.2 \
+ R-mathlib=~3.6.2 \
+ R-dev=~3.6.2
+
+ENV R_DEPS g++ \
+ libxml2-dev \
+ make \
+ cmake \
+ linux-headers \
+ cairo-dev \
+ libxmu-dev \
+ pango-dev \
+ perl \
+ tiff-dev \
+ gcc \
+ gfortran \
+ icu-dev \
+ libjpeg-turbo \
+ libpng-dev \
+ openblas-dev \
+ pcre-dev \
+ readline-dev \
+ xz-dev \
+ zlib-dev \
+ bzip2-dev \
+ curl-dev \
+ libexecinfo-dev \
+ git
+
+RUN echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/main" > /etc/apk/repositories && \
+ echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/community" >> /etc/apk/repositories && \
+ apk add --update --no-cache ${R_PKGS} ${R_DEPS}
+
+CMD ["R", "--no-save"]
diff --git a/src/.docker_modules/r/3.6.2/docker_init.sh b/src/.docker_modules/r/3.6.2/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..78d50296b2f41e54690986e4d7c61a8b7f4c4419
--- /dev/null
+++ b/src/.docker_modules/r/3.6.2/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/r-base:3.6.2
+docker build src/.docker_modules/r/3.6.2 -t 'lbmc/r-base:3.6.2'
+docker push lbmc/r-base:3.6.2
diff --git a/src/.docker_modules/r/4.0.0/Dockerfile b/src/.docker_modules/r/4.0.0/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..6bfa98a516d2cf1ca66d07ffc8749ad1c57240d4
--- /dev/null
+++ b/src/.docker_modules/r/4.0.0/Dockerfile
@@ -0,0 +1,38 @@
+FROM alpine:3.12.0
+MAINTAINER Lauret Modolo
+
+ENV R_PKGS R=~4.0.0 \
+ R-mathlib=~4.0.0 \
+ R-dev=~4.0.0
+
+ENV R_DEPS g++ \
+ libxml2-dev \
+ make \
+ cmake \
+ linux-headers \
+ cairo-dev \
+ libxmu-dev \
+ pango-dev \
+ perl \
+ tiff-dev \
+ gcc \
+ gfortran \
+ icu-dev \
+ libjpeg-turbo \
+ libpng-dev \
+ openblas-dev \
+ pcre-dev \
+ readline-dev \
+ xz-dev \
+ zlib-dev \
+ bzip2-dev \
+ curl-dev \
+ libexecinfo-dev \
+ git
+
+RUN echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/main" > /etc/apk/repositories && \
+ echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/community" >> /etc/apk/repositories && \
+ sed -i -e 's/v[[:digit:]]\..*\//edge\//g' /etc/apk/repositories && \
+ apk add --update --no-cache ${R_PKGS} ${R_DEPS}
+
+CMD ["R", "--no-save"]
diff --git a/src/.docker_modules/r/4.0.0/docker_init.sh b/src/.docker_modules/r/4.0.0/docker_init.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2f7d058612659d3b56e6d4b22e0c94798c01ccac
--- /dev/null
+++ b/src/.docker_modules/r/4.0.0/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/r-base:4.0.0
+docker build src/.docker_modules/r/4.0.0 -t 'lbmc/r-base:4.0.0'
+docker push lbmc/r-base:4.0.0
diff --git a/src/.singularity_psmn b/src/.singularity_psmn
new file mode 120000
index 0000000000000000000000000000000000000000..a5b71da334132bfa76cd674fa170744c49a129c7
--- /dev/null
+++ b/src/.singularity_psmn
@@ -0,0 +1 @@
+/scratch/Bio/singularity
\ No newline at end of file
diff --git a/src/.update_config.sh b/src/.update_config.sh
index 3e7c6a1e8f6a7b9c01b5d27bb8fc05cb14a4a633..2ea29fcf25727fdddaa062fbc7c047f89f9e4af5 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -17,3 +17,16 @@ fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p
# we update the psmn module to conda
fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"\n\s*module = "(.*)/(.*)"|beforeScript = "source \$baseDir/.conda_psmn.sh"\n conda = "\$baseDir/.conda_envs/\L\1_\2"|mg' -i {}
+
+# we update the psmn queue to new cluster
+fd ".*config" src/ -x perl -0777pe 's|E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F|CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128|monointeldeb128|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|openmp16|openmp32|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|cpus = 16|cpus = 32|mg' -i {}
+fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
+
+# we update the psmn config to singularity
+fd ".*config" src/ -x perl -0777pe 's|psmn{|psmn{\n singularity.enabled = true\n singularity.cacheDir = "$baseDir/.singularity_psmn/"\n singularity.runOptions = "--bind /Xnfs,/scratch"|mg' -i {}
+fd ".*config" src/ -x perl -0777pe 's|beforeScript.*conda.*(\n\s*clusterOptions = "-cwd -V".*)(container .*executor = "sge")|\2\1\2|gs' -i {}
+fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*scratch = true(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}
+fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*stageInMode = "copy"\n\s*stageOutMode = "rsync"(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 8515e966fdab38145cb9508d3a72f5830f464ebc..791d4b0a675c1576156a847349115a0e6301cf4b 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -129,6 +129,7 @@ samtools index ${file_id}_sorted.bam
"""
}
+sorted_bam_files.into{sorted_bam_htseq, sorted_bam_coverage}
/* HTseq */
@@ -136,7 +137,7 @@ process sort_bam {
tag "$file_id"
input:
- set file_id, file(bam) from sorted_bam_files
+ set file_id, file(bam) from sorted_bam_htseq
output:
set file_id, "*_htseq.bam" into sorted_bam_files_2
@@ -188,3 +189,22 @@ htseq-count ${bam[0]} ${gtf} \
"""
}
+
+process coverage {
+ tag "$file_id"
+ publishDir "${params.output}/05_coverage/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from sorted_bam_coverage
+
+ output:
+ file "*.bw" into coverage_files
+
+ script:
+"""
+bash src/norm_coverage.sh -b ${bam} \
+ -o {file_id}.bw \
+ --binSize 1 \
+ -p ${cpus} 8
+"""
+}
diff --git a/src/fasta_sampler.nf b/src/fasta_sampler.nf
new file mode 100644
index 0000000000000000000000000000000000000000..d1200ed496c77756cde525835f581b71b2528990
--- /dev/null
+++ b/src/fasta_sampler.nf
@@ -0,0 +1,18 @@
+Channel
+ .fromPath( "data/tiny_dataset/fasta/*.fasta" )
+ .set { fasta_file }
+
+process sample_fasta {
+ publishDir "results/sampling/", mode: 'copy'
+
+ input:
+file fasta from fasta_file
+
+ output:
+file "*_sample.fasta" into fasta_sample
+
+ script:
+"""
+head ${fasta} > ${fasta.baseName}_sample.fasta
+"""
+}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 7a3302d7d6068d7e2bd71481064b99a91dc9da4f..a04494e663516f7643d786da08e7e6229a5b4f37 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fasta_from_bed {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fasta_from_bed {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bedtools_2.25.0"
+ container = "lbmc/bedtools:2.25.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -46,7 +48,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index c67cef25d2ad1a3d9c01a93ce37b6c6e1ce6f74f..ccf47042bc019c4d8a601543ec7bc7213cbb738c 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie_1.2.2"
+ container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index ac4c35e46a11ddab8fe6c6dc33f67dd09e99eeae..e6c7c6dadd4625a6affeabcfc68e50aa30f8f227 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie/1.2.2"
+ container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index ac4c35e46a11ddab8fe6c6dc33f67dd09e99eeae..e6c7c6dadd4625a6affeabcfc68e50aa30f8f227 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie/1.2.2"
+ container = "lbmc/bowtie:1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index dd1e5e0648c2c38159cce2841d2201bd05d79e29..773c5eae572785d6a7fea6ed1e3ccb9b8d14e00d 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "20GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index c4b0fdd102fd74fa4151e7543e44f42ecfcb3cdf..b9f515f11cbc300b8208d7033a90f40bb75ef774 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index c4b0fdd102fd74fa4151e7543e44f42ecfcb3cdf..b9f515f11cbc300b8208d7033a90f40bb75ef774 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 689b5fa2de7db12f2691efd89221fbaf66d7a950..b3b90059b1cb324f5b792f811079002aabd8acd2 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bwa_0.7.17"
+ container = "lbmc/bwa:0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index b2e198a0629c28595aaf4fedc7f83e7e5dd9232c..b28e5b9cf21573fc04a6fcf103fff13fee1b8ffa 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/bwa_0.7.17"
+ container = "lbmc/bwa:0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index ed42799d9cc1e9a8d3c532a61f3918d3c727cfbd..ea069fd8c3e413f1bc28bad77b6d427b1f41e29f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -1,10 +1,10 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -14,22 +14,24 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -39,14 +41,14 @@ 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"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index ed42799d9cc1e9a8d3c532a61f3918d3c727cfbd..ea069fd8c3e413f1bc28bad77b6d427b1f41e29f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -1,10 +1,10 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -14,22 +14,24 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: adaptor_removal {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: adaptor_removal {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -39,14 +41,14 @@ 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"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 8c158c0e72a5927b67cf1a4c106f7e22555e1cba..d69a7021effe93ae0c3ede2c8b2f9adc05362025 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -1,10 +1,10 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -14,22 +14,24 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: trimming {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -39,14 +41,14 @@ 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"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 8c158c0e72a5927b67cf1a4c106f7e22555e1cba..d69a7021effe93ae0c3ede2c8b2f9adc05362025 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -1,10 +1,10 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
@@ -14,22 +14,24 @@ profiles {
singularity.cacheDir = "./bin/"
process {
withName: trimming {
- container = "lbmc/cutadapt:2.4"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ container = "lbmc/cutadapt:2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -39,14 +41,14 @@ 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"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 2cbf9d68a467a99ed2bdd59db667c7b5533c42be..9dd57e691ea71e368e4835e5b37d6a8c8c04a175 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_bam {
@@ -28,28 +28,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 16
- memory = "30GB"
- time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
- }
- withName: bam_to_bigwig {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "deeptools/3.0.2"
+ container = "lbmc/deeptools:3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -67,7 +58,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: bam_to_bigwig {
container = "lbmc/deeptools:3.0.2"
@@ -78,7 +69,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index d1c05456c37ccf67b9a21ff48da719b45060aa50..8c9c1b7a6cf50cb012569ffabc605d666af11fac 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: compute_matrix {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: compute_matrix {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/deeptools_3.0.2"
+ container = "lbmc/deeptools:3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index c10e0edc66a119775a2600b2890eede8824a9468..9320784680c101ee6bf0b8fa77aff11afcd0f2a4 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: plot_profile {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: plot_profile {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/deeptools_3.0.2"
+ container = "lbmc/deeptools:3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index d2ef420f462fcc3b43dfd29b3c24baeb0afc86db..dc9bf8cde93bdc0e51dc318d2e4d9f9fb321ae82 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastp_fastq {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastp_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastp_0.19.7"
+ container = "lbmc/fastp:0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +49,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index d2ef420f462fcc3b43dfd29b3c24baeb0afc86db..dc9bf8cde93bdc0e51dc318d2e4d9f9fb321ae82 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastp_fastq {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastp_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastp_0.19.7"
+ container = "lbmc/fastp:0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +49,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 743c85ec616152e94ee9da40e254c8a6a826416a..5f12694b8f34eea4b873cd8ddc4cccdc680002a9 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+ container = "lbmc/fastqc:0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +49,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 743c85ec616152e94ee9da40e254c8a6a826416a..5f12694b8f34eea4b873cd8ddc4cccdc680002a9 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+ container = "lbmc/fastqc:0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +49,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index ab38148c140ddf8691df3b1ded842c328ad9f027..5d154dd49c0a40d51046a5134e71621a0f6db6f6 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/hisat2_2.1.0"
+ container = "lbmc/hisat2:2.1.0"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index b3e4df5797cd3b98c7c28632f44944f50e5188fc..964db5213282012246a0fbfe63332abd37f53e5b 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -27,10 +27,10 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index b3e4df5797cd3b98c7c28632f44944f50e5188fc..964db5213282012246a0fbfe63332abd37f53e5b 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -27,10 +27,10 @@ profiles {
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +48,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 2eebc16c3af08c2bcf5924b42a6ed346a421a4f4..931ca7848e8c382befe60caf281b46dd723d6f19 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -28,26 +28,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
- }
- withName: counting {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "htseq/0.11.2"
+ container = "lbmc/htseq:0.11.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -65,7 +57,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: counting {
container = "lbmc/htseq:0.11.2"
@@ -76,7 +68,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 3ca188a0d614661f971529630df0870617b39f92..52d83cf298c9daee3d767a8b93ba6be28076d3e2 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName index_fasta {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 04b61fea005056198f09c2a6b8418608dd1c94b4..839ae33192e5c9ca4c72ff83f64e89abed05d5ac 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 04b61fea005056198f09c2a6b8418608dd1c94b4..839ae33192e5c9ca4c72ff83f64e89abed05d5ac 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+ container = "lbmc/kallisto:0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 35186c52c4701124f937a5daa625e72e8cb0a85e..d3cbbdb98ced18dd2756bc4f96b18f0e6d28647a 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: peak_calling {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: peak_calling {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/macs2_2.1.2"
+ container = "lbmc/macs2:2.1.2"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 1cb17b7cd1cdb912c835877e043d1af80f34002d..c8fe4a1d9c3cc85287d80a6e578b780178ac6dd6 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -1,7 +1,7 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -29,30 +29,20 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
- }
- withName: multiqc {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "multiqc/1.7"
+ container = "lbmc/multiqc:1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ pollInterval = "60sec"
+ queue = "monointeldeb128"
}
}
}
@@ -70,7 +60,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: multiqc {
container = "lbmc/multiqc:1.7"
@@ -81,7 +71,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index ba1bbe7c996ec4f7ae9ce1e2c4cefbcb883087b1..641a65e3d359b581b9860b548fe71bfa55a6a0e7 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastqc_fastq {
@@ -28,30 +28,20 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastqc_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/fastqc_0.11.5"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
- }
- withName: multiqc {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "multiqc/1.7"
+ container = "lbmc/multiqc:1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1.70
- pollInterval = '60sec'
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ pollInterval = "60sec"
+ queue = "monointeldeb128"
}
}
}
@@ -69,7 +59,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: multiqc {
container = "lbmc/multiqc:1.7"
@@ -80,7 +70,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 4a500bb9c52cecf86bca242df15b8024f65fe632..dea6fa7b77851ace3272ac460a9db888acb2bb31 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: compute_mappability {
@@ -36,36 +36,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: compute_mappability {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/music_6613c53"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
- }
- withName: music_preprocessing {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "music/6613c53"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
- }
- withName: music_computation{
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "music/6613c53"
+ container = "lbmc/music:6613c53"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -83,7 +65,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: music_preprocessing {
container = "lbmc/music:6613c53"
@@ -94,7 +76,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: music_computation{
container = "lbmc/music:6613c53"
@@ -105,7 +87,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d5d3c7814b253b5869e799f7268f6985972d3d2c..86f57dde734750c4e55857b645cd60f231dd72ed 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/rsem_1.3.0"
+ container = "lbmc/rsem:1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index bde03fc98ab828ebc58ee268a2dd9b1fe342f77b..a959b00faf62fd63965be66d1efbab61c70b1772 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/rsem_1.3.0"
+ container = "lbmc/rsem:1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index bde03fc98ab828ebc58ee268a2dd9b1fe342f77b..a959b00faf62fd63965be66d1efbab61c70b1772 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/rsem_1.3.0"
+ container = "lbmc/rsem:1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 3a20b7e120fceb5532a82555829a84e3fe5a435a..da8f84fc81c1eb17176d16fd04af21c886661477 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_bam {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+ container = "lbmc/sambamba:0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 8612de4aacf04c0ee6eb41e318b118cf3e72b4a6..610573272475384df4ad0d0ee46f7dd053f1aa3c 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+ container = "lbmc/sambamba:0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 4ce0bcb06a61c5941223381c16f1996c48ee67b1..e9df7d6965eb7a88c9f8d196888c05a8ec6d8c03 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: split_bam {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: split_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+ container = "lbmc/sambamba:0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 66f3051148ad1bcfddf4ca73c85b2b9040a3c963..e35185c15749ec3a4c91d4497e29391cb6180018 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: dedup_sam {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: dedup_sam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samblaster_0.1.24"
+ container = "lbmc/sambamba:0.6.7"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index b2cdd8e5202f179833e877e8346430e01826fc17..dfd7f8bf183336f1168e3c93e755f153ca2f410d 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: filter_bam {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: filter_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 3e2156e16ee72fddb0b317c0dd22e3342fbe1cd8..173af8fe0940a96d9fe03c0179eb62aaca76dace 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_bam {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +49,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index dd7cd38b2fe475ad409444ad2406e08c6a21b6cb..48f18580754cd776a7c409206963dbd5a55a50f8 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 6c8ca3e963019002889a8f1ee3c3bb1166df7737..757a946a3888bc801aeef5a68eb90c3695197192 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: split_bam {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: split_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
+ container = "lbmc/samtools:1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +49,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index e6e80c5dffe098e1e893af480600a6ce40661d03..4287e92f36e6b2774f39ce3d38191c76881f312f 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: fastq_dump {
@@ -20,16 +20,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: fastq_dump {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
+ container = "lbmc/sratoolkit:2.8.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -47,7 +49,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index 34683657e3856d700dfc357591f46477598de70b..503c1b8c9fa6c21261530c8d3f9c78a5a30c207e 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: index_fasta {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: index_fasta {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/star_2.7.3a"
+ container = "lbmc/star:2.7.3a"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "20GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index 615404c4928c2281722ad15b50055b37eddfb7aa..d9d43b943740d4f714e05075827b843a606e02e3 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/star_2.7.3a"
+ container = "lbmc/star:2.7.3a"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index 615404c4928c2281722ad15b50055b37eddfb7aa..d9d43b943740d4f714e05075827b843a606e02e3 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: mapping_fastq {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: mapping_fastq {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/star_2.7.3a"
+ container = "lbmc/star:2.7.3a"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -47,7 +49,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 68147001c4c8d630210e9c617b193d977212721c..2d09601a5bc48e9ff0f65edde7fb56d978ffd90b 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: sort_bam {
@@ -28,26 +28,18 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: sort_bam {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/samtools_1.7"
- executor = "sge"
- clusterOptions = "-cwd -V"
- cpus = 1
- memory = "20GB"
- time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
- }
- withName: counting {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "subread/1.6.4"
+ container = "lbmc/subread:1.6.4"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
}
}
@@ -65,7 +57,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: counting {
container = "lbmc/subread:1.6.4"
@@ -76,7 +68,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index a9f28632bc1552a9d497f9ddc8b7f73e26b9f6fe..f5ca80843af2ead8ca438a839765a77497e7a337 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
- cpus = 16
+ cpus = 32
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 012b3f3afb518677d0aae318979701d32861cca5..374112e5218fa5916800f3c92bd6f989d59a9aa2 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: trimming {
@@ -20,17 +20,19 @@ profiles {
}
}
psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
process{
withName: trimming {
- beforeScript = "source $baseDir/.conda_psmn.sh"
- conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
- cpus = 16
+ cpus = 32
memory = "5GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -48,7 +50,7 @@ profiles {
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}
diff --git a/src/norm_coverage.sh b/src/norm_coverage.sh
new file mode 100644
index 0000000000000000000000000000000000000000..8dcf4c835e1639bbec5a84f10aadd1a2190f4e3c
--- /dev/null
+++ b/src/norm_coverage.sh
@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+
+set -e
+
+usage() { echo "Usage: $0 -b <bamfile.bam> -o <outputName> --binSize <int> -p <CPUs>" 1>&2; exit 1; }
+
+cpus=4
+binSize=1
+
+while getopts "b:o:binSize:p:" arg; do
+ case $arg in
+ -h)
+ echo "usage"
+ ;;
+ -b)
+ bam=$OPTARG
+ ;;
+ -o)
+ output=$OPTARG
+ ;;
+ --binSize)
+ binSize=$OPTARG
+ ;;
+ -p)
+ cpus=$OPTARG
+ ;;
+ esac
+done
+
+hg38=$(samtools view ${bam} | awk '{print $1}' | sort | uniq | wc -l)
+factor=$(echo "1000000/($hg38)" | bc -l)
+echo "hg38 counts : $hg38"
+echo "scaling factor : $factor\n"
+bamCoverage -p ${cpus} --scaleFactor ${factor} --binSize ${binSize} -b ${bam} -o ${output}
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
new file mode 100644
index 0000000000000000000000000000000000000000..fadfceb4bef905feafb1df7fbf1f2d3101ebb822
--- /dev/null
+++ b/src/solution_RNASeq.config
@@ -0,0 +1,171 @@
+profiles {
+ docker {
+ docker.temp = "auto"
+ docker.enabled = true
+ process {
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ cpus = 1
+ }
+ withName: trimming {
+ cpus = 4
+ container = "lbmc/urqt:d62c1f8"
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ cpus = 1
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ process {
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ cpus = 1
+ }
+ withName: trimming {
+ cpus = 4
+ container = "lbmc/urqt:d62c1f8"
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ cpus = 1
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.singularity_psmn/"
+ singularity.runOptions = "--bind /Xnfs,/scratch"
+ process{
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = "monointeldeb128"
+ }
+ withName: trimming {
+ container = "lbmc/urqt:d62c1f8"
+ scratch = true
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
+
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = "monointeldeb128"
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 32
+ memory = "30GB"
+ time = "24h"
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
+ }
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.cacheDir = "$baseDir/.singularity_in2p3/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: adaptor_removal {
+ container = "lbmc/cutadapt:2.1"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = "huge"
+ }
+ withName: trimming {
+ container = "lbmc/urqt:d62c1f8"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = "huge"
+ }
+ withName: fasta_from_bed {
+ container = "lbmc/bedtools:2.25.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ cpus = 1
+ queue = "huge"
+ }
+ withName: index_fasta {
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = "huge"
+ }
+ withName: mapping_fastq {
+ container = "lbmc/kallisto:0.44.0"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
+ cpus = 1
+ queue = "huge"
+ }
+ }
+ }
+}
diff --git a/src/solution_RNASeq.nf b/src/solution_RNASeq.nf
new file mode 100644
index 0000000000000000000000000000000000000000..73940d6595aa3828629292cff067fcf20d3603f0
--- /dev/null
+++ b/src/solution_RNASeq.nf
@@ -0,0 +1,111 @@
+log.info "fastq files : ${params.fastq}"
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
+
+Channel
+ .fromPath( params.fasta )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+ .set { fasta_files }
+Channel
+ .fromPath( params.bed )
+ .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+ .set { bed_files }
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process adaptor_removal {
+ tag "$pair_id"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+
+ cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+ """
+}
+
+process trimming {
+ tag "${reads}"
+ publishDir "results/fastq/trimming/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_cut
+
+ output:
+ set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+
+ script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+--in ${reads[0]} --inpair ${reads[1]} \
+--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+> ${pair_id}_trimming_report.txt
+"""
+}
+
+process fasta_from_bed {
+ tag "${bed.baseName}"
+ publishDir "results/fasta/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files
+ file bed from bed_files
+
+ output:
+ file "*_extracted.fasta" into fasta_files_extracted
+
+ script:
+"""
+bedtools getfasta -name \
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
+"""
+}
+
+process index_fasta {
+ tag "$fasta.baseName"
+ publishDir "results/mapping/index/", mode: 'copy'
+
+ input:
+ file fasta from fasta_files_extracted
+
+ output:
+ file "*.index*" into index_files
+ file "*_kallisto_report.txt" into index_files_report
+
+ script:
+"""
+kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
+2> ${fasta.baseName}_kallisto_report.txt
+"""
+}
+
+process mapping_fastq {
+ tag "$reads"
+ publishDir "results/mapping/quantification/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files_trim
+ file index from index_files.collect()
+
+ output:
+ file "*" into counts_files
+
+ script:
+"""
+mkdir ${pair_id}
+
+kallisto quant -i ${index} -t ${task.cpus} \
+--bias --bootstrap-samples 100 -o ${pair_id} \
+${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
+"""
+}
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 226acd9fd45046d7e24d829de16447d81873c8d4..734a7410c3f3d2425a98b2f1462faee929dc68e1 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -1,6 +1,6 @@
profiles {
docker {
- docker.temp = 'auto'
+ docker.temp = "auto"
docker.enabled = true
process {
withName: build_synthetic_bed {
@@ -125,7 +125,7 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: fasta_from_bed {
beforeScript = "source $baseDir/.conda_psmn.sh"
@@ -135,106 +135,106 @@ profiles {
cpus = 1
memory = "20GB"
time = "12h"
- queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+ queue = "monointeldeb128"
}
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "20GB"
time = "12h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: mapping_fastq_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: bam_2_fastq_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: sort_bam_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: index_bam_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: mapping_fastq_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: bam_2_fastq_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: sort_bam_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
withName: index_bam_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
- cpus = 16
+ cpus = 32
memory = "30GB"
time = "24h"
- queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
- penv = 'openmp16'
+ queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
+ penv = "openmp32"
}
}
}
@@ -251,7 +251,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
process{
@@ -263,7 +263,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
@@ -273,7 +273,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
@@ -283,7 +283,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: mapping_fastq_paired {
container = "lbmc/bowtie2:2.3.4.1"
@@ -293,7 +293,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: bam_2_fastq_paired {
container = "lbmc/samtools:1.7"
@@ -303,7 +303,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: sort_bam_paired {
container = "lbmc/samtools:1.7"
@@ -313,7 +313,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: index_bam_paired {
container = "lbmc/samtools:1.7"
@@ -323,7 +323,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: mapping_fastq_single {
container = "lbmc/bowtie2:2.3.4.1"
@@ -333,7 +333,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: bam_2_fastq_single {
container = "lbmc/samtools:1.7"
@@ -343,7 +343,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: sort_bam_single {
container = "lbmc/samtools:1.7"
@@ -353,7 +353,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
withName: index_bam_single {
container = "lbmc/samtools:1.7"
@@ -363,7 +363,7 @@ profiles {
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
- queue = 'huge'
+ queue = "huge"
}
}
}