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C2 Nextflow

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C2 Nextflow

Quick-Start

1. Load relevant modules

module load ris module load nextflow/24.10.0 apptainer/1.3.4

2. Obtain the default nextflow.config file for use on Compute2.

wget https://raw.githubusercontent.com/WashU-IT-RIS/c2-ris-app-config-templates/refs/heads/main/nextflow/nextflow.config

  • This file can be placed anywhere you like with whatever name you like, provided you use -c /path/to/your.config when executing Nextflow.

  • The default location is $HOME/.config/nextflow/, in a file named nextflow.config

  • Create a temporary output directory for Nextflow.

    mkdir -p /scratch2/fs1/allocation_name/nextflow/output

  • This can be other locations, like a RIS Storage platform.

  • scratch2 is preferred (and faster) if there is access available.

  • allocation_name is the name of the scratch allocation. E.g. ris

3. Execute a test pipeline

Make sure that Nextflow commands are run as part of a job, not on the login clients.

nextflow run nf-core/rnaseq \ -r 3.15.1 \ -profile test \ -c ./nextflow.config \ --outdir /scratch2/fs1/${allocation_name}/nextflow/output

  • -r sets the release version

  • -c optionally sets the NextFlow config path.

    • Defaults to $HOME/.config/nextflow/nextflow.config

  • --outdir sets the root temp directory where NextFlow work is performed

  • IMPORTANT: set the allocation_name variable.

In another terminal window, you can verify that jobs are running in SLURM rather than locally using sacct.

Additional Information

  • RIS does not support DSL1-based Nextflow pipelines.