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Merge branch 'master' into master
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commit
06bd1ab79e
8 changed files with 35 additions and 41 deletions
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@ -18,9 +18,9 @@ process {
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params {
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igenomes_base = '/nfsmounts/igenomes'
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max_memory = 1024.GB
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max_memory = 128.GB
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max_cpus = 28
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max_time = 168.h
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max_time = 48.h
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}
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weblog{
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@ -8,25 +8,16 @@ params {
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process {
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executor = 'slurm'
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module = 'singularity/3.2.1'
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queue = 'c'
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queue = { task.memory <= 170.GB ? 'c' : 'm' }
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clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
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}
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singularity.enabled = true
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params {
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target_qos = 'medium'
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params.max_cpus = 36
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params.max_memory = 170.GB
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igenomesIgnore = true
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}
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if (params.target_qos == 'short') {
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params.max_time = 8.h
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process.clusterOptions = '--qos short'
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} else if (params.target_qos == 'medium') {
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params.max_time = 2.d
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process.clusterOptions = '--qos medium'
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} else {
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params.max_time = 14.d
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process.clusterOptions = '--qos long'
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}
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params.max_cpus = 36
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params.max_memory = 4.TB
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igenomes_ignore = true
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igenomesIgnore = true //deprecated
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}
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@ -55,7 +55,8 @@ params {
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awsregion = "us-west-2"
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awsqueue = "nextflow"
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igenomesIgnore = true
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igenomes_ignore = true
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igenomesIgnore = true //deprecated
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fc_extra_attributes = 'gene_name'
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fc_group_features = 'gene_id'
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@ -16,7 +16,8 @@ process {
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}
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params {
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igenomesIgnore = true
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igenomes_ignore = true
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igenomesIgnore = true //deprecated
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max_memory = 750.GB
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max_cpus = 80
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max_time = 336.h
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@ -18,7 +18,8 @@ process {
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}
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params {
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igenomesIgnore = true
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igenomes_ignore = true
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igenomesIgnore = true //deprecated
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saveReference = true
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max_memory = 64.GB
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max_cpus = 20
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@ -19,5 +19,6 @@ params {
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max_cpus = 32
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max_memory = 128.GB
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max_time = 192.h
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igenomesIgnore = true
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igenomes_ignore = true
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igenomesIgnore = true //deprecated
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}
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@ -16,7 +16,8 @@ process {
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}
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params {
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igenomesIgnore = true
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igenomes_ignore = true
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igenomesIgnore = true //deprecated
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max_memory = 256.GB
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max_cpus = 28
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max_time = 24.h
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@ -4,38 +4,36 @@ All nf-core pipelines have been successfully configured for use on the tars clus
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To use, run the pipeline with `-profile pasteur`. This will download and launch the [`pasteur.config`](../conf/pasteur.config) which has been pre-configured with a setup suitable for the Pasteur cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
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## Running the workflow on the Pasteur cluster
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Nextflow is not installed by default on the Pasteur cluster.
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- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
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Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
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Nextflow shouldn't run directly on the submission node but on a compute node.
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The compute nodes don't have access to internet so you need to run it offline.
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To do that:
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1. Create a virtualenv to install nf-core
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```bash
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module purge
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module load Python/3.6.0
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module load java
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module load singularity
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cd /path/to/nf-core/workflows
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virtualenv .venv -p python3
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. .venv/bin/activate
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```
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```bash
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module purge
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module load Python/3.6.0
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module load java
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module load singularity
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cd /path/to/nf-core/workflows
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virtualenv .venv -p python3
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. .venv/bin/activate
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```
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2. Install nf-core: [here](https://nf-co.re/tools#installation)
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3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use)
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4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage)
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5. Run nextflow on a compute node:
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4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base)
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5. Run nextflow on a compute node:
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```bash
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# create a terminal
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tmux
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tmux
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# Get a compute node
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salloc
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# Run nextflow workflow
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nextflow run \\
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/path/to/pipeline-dir/from/step/3/workflow \\
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-resume
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-resume
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-profile pasteur \\
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-with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
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--email my-email@pasteur.fr \\
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