diff --git a/docs/abims.md b/docs/abims.md index 2628abb..c25c80f 100644 --- a/docs/abims.md +++ b/docs/abims.md @@ -23,23 +23,50 @@ Nextflow manages each process as a separate job that is submitted to the cluster Nextflow shouldn't run directly on the submission node but on a compute node. Run nextflow from a compute node: ```bash -# Login to a compute node -srun --pty bash - # Load the dependencies if not done before module load nextflow slurm-drmaa graphviz # Run a downloaded/git-cloned nextflow workflow from -nextflow run \\ -/path/to/nf-core/workflow \\ --resume --profile abims \\ ---email my-email@example.org \\ +srun nextflow run \ +/path/to/nf-core/workflow \ +-profile abims \ +--email my-email@example.org \ -c my-specific.config ... -# Or use the nf-core client -nextflow run nf-core/rnaseq ... +# Or use let nf-core client download the workflow +srun nextflow run nf-core/rnaseq -profile abims ... + +# To launch in background +sbatch --wrap "nextflow run nf-core/rnaseq -profile abims ..." +``` + +Or write a sbatch script + +> nfcore-rnaseq.sh + +```bash +#!/bin/bash +#SBATCH -p fast +#SBATCH --mem=4G + +module load nextflow slurm-drmaa graphviz +nextflow run nf-core/rnaseq -profile abims ... +``` + +Launch on the cluster with sbatch: + +```bash +sbatch nfcore-rnaseq.sh +``` + +### Hello, world! + +nf-core provides some test for each workflow: + +```bash +module load nextflow slurm-drmaa graphviz +nextflow run nf-core/rnaseq -profile abims,test ``` ## Singularity images mutualized directory