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38 lines
1.4 KiB
Markdown
38 lines
1.4 KiB
Markdown
# 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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