diff --git a/conf/abims.config b/conf/abims.config new file mode 100644 index 0000000..47be8cd --- /dev/null +++ b/conf/abims.config @@ -0,0 +1,24 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'The ABiMS cluster profile' + config_profile_contact = 'Gildas Le Corguillé (@lecorguille)' + config_profile_url = 'https://abims.sb-roscoff.fr' +} + +singularity { + enabled = true + autoMounts = true + runOptions = '-B /scratch:/scratch -B /scratch2:/scratch2 -B /shared:/shared' +} + +process { + executor = 'slurm' +} + +params { + igenomes_ignore = true + igenomesIgnore = true //deprecated + max_memory = 750.GB + max_cpus = 200 + max_time = 24.h +} diff --git a/docs/abims.md b/docs/abims.md new file mode 100644 index 0000000..a3298e5 --- /dev/null +++ b/docs/abims.md @@ -0,0 +1,46 @@ +# nf-core/configs: ABiMS Configuration + +All nf-core pipelines have been successfully configured for use on the ABiMS cluster. + +To use, run the pipeline with `-profile abims`. This will download and launch the [`abims.config`](../conf/abims.config) which has been pre-configured with a setup suitable for the ABiMS 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. + +## Request an account +You will need an account to use the HPC cluster on ABiMS in order +to run the pipeline. If in doubt see [http://abims.sb-roscoff.fr/account](http://abims.sb-roscoff.fr/account). + +## Running the workflow on the ABiMS cluster + +Nextflow is installed on the ABiMS cluster. Some documentation is available on the [ABiMS website](http://abims.sb-roscoff.fr/resources/cluster/howto#nextflow). + +You need to activate it like this: + +```bash +module load nextflow/20.04.1 slurm-drmaa/1.0.8 +``` + +Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command. +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/20.04.1 slurm-drmaa/1.0.8 + +# Run a downloaded/git-cloned nextflow workflow from +nextflow run \\ +/path/to/nf-core/workflow \\ +-resume +-profile abims \\ +--email my-email@example.org \\ +-c my-specific.config +... + +# Or use the nf-core client +nextflow run nf-core/rnaseq ... +``` + +## Databanks + +A local copy of several genomes are available in `/shared/bank` directory.