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@ -91,6 +91,7 @@ Currently documentation is available for the following clusters:
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* [CRICK](docs/crick.md)
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* [CZBIOHUB_AWS](docs/czbiohub.md)
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* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
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* [GENOUEST](docs/genouest.md)
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* [GIS](docs/gis.md)
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* [HEBBE](docs/hebbe.md)
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* [KRAKEN](docs/kraken.md)
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23
conf/genouest.config
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23
conf/genouest.config
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@ -0,0 +1,23 @@
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//Profile config names for nf-core/configs
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params {
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config_profile_description = 'The GenOuest cluster profile'
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config_profile_contact = 'Anthony Bretaudeau (@abretaud)'
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config_profile_url = 'https://www.genouest.org'
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}
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singularity {
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enabled = true
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autoMounts = true
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runOptions = '-B /scratch:/scratch -B /local:/local -B /db:/db'
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}
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process {
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executor = 'slurm'
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}
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params {
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igenomesIgnore = true
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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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}
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38
docs/genouest.md
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38
docs/genouest.md
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@ -0,0 +1,38 @@
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# nf-core/configs: GenOuest Configuration
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All nf-core pipelines have been successfully configured for use on the GenOuest cluster.
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To use, run the pipeline with `-profile genouest`. This will download and launch the [`genouest.config`](../conf/genouest.config) which has been pre-configured with a setup suitable for the GenOuest 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 GenOuest cluster
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Nextflow is installed on the GenOuest cluster. Some documentation is available on the [GenOuest website](https://www.genouest.org/howto/#nextflow).
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You need to activate it like this:
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```bash
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source /local/env/envnextflow-19.07.0.sh
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```
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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. Run nextflow from a compute node:
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```bash
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# Login to a compute node
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srun --pty bash
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# Load the dependencies if not done before
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source /local/env/envnextflow-19.07.0.sh
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# Run a downloaded/git-cloned nextflow workflow from
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nextflow run \\
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/path/to/nf-core/workflow \\
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-resume
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-profile genouest \\
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--email my-email@example.org \\
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-c my-specific.config
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...
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# Or use the nf-core client
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nextflow run nf-core/rnaseq ...
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```
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@ -21,6 +21,7 @@ profiles {
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crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
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czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
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czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
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genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" }
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gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
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hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
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kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" }
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@ -43,6 +44,7 @@ params {
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// This is a groovy map, not a nextflow parameter set
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hostnames = [
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crick: ['.thecrick.org'],
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genouest: ['.genouest.org'],
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uppmax: ['.uppmax.uu.se']
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]
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}
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