From 23ba1c58b1aaf0c5f3e38533d3b8a00de26c4546 Mon Sep 17 00:00:00 2001 From: lecorguille Date: Thu, 22 Oct 2020 23:17:55 +0200 Subject: [PATCH] Add ABiMS - NXF_SINGULARITY_CACHEDIR --- docs/abims.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/docs/abims.md b/docs/abims.md index 43896ab..87cc5c4 100644 --- a/docs/abims.md +++ b/docs/abims.md @@ -16,7 +16,7 @@ Nextflow is installed on the ABiMS cluster. Some documentation is available on t You need to activate it like this: ```bash -module load nextflow/20.04.1 slurm-drmaa/1.0.8 +module load nextflow slurm-drmaa graphviz ``` Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command. @@ -27,7 +27,7 @@ Nextflow shouldn't run directly on the submission node but on a compute node. Ru srun --pty bash # Load the dependencies if not done before -module load nextflow/20.04.1 slurm-drmaa/1.0.8 +module load nextflow slurm-drmaa graphviz # Run a downloaded/git-cloned nextflow workflow from nextflow run \\ @@ -42,6 +42,12 @@ nextflow run \\ nextflow run nf-core/rnaseq ... ``` +## Singularity images mutualized directory + +To reduce the disk usage, nf-core images can be stored in a mutualized directory: `/shared/software/singularity/images/nf-core/` + +The environment variable `NXF_SINGULARITY_CACHEDIR: /shared/data/cache/nextflow` will indicate this directory to nextflow. + ## Databanks -A local copy of several genomes are available in `/shared/bank` directory. +A local copy of several genomes are available in `/shared/bank/` directory.