From e7f8189dfc95b07e34f8ea33ac51cc17d7a79d10 Mon Sep 17 00:00:00 2001 From: Ashley S Doane Date: Thu, 11 Mar 2021 13:52:11 -0500 Subject: [PATCH 1/3] Create wcm.config --- conf/wcm.config | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 conf/wcm.config diff --git a/conf/wcm.config b/conf/wcm.config new file mode 100644 index 0000000..38cd3d1 --- /dev/null +++ b/conf/wcm.config @@ -0,0 +1,28 @@ +singularityDir = "/athena/elementolab/scratch/reference/.singularity/singularity_images_nextflow" + +params { + config_profile_description = 'Weill Cornell Medicine, Scientific Computing Unit Slurm cluster profile provided by nf-core/configs' + config_profile_contact = 'Ashley Stephen Doane, PhD (@DoaneAS)' + igenomes_base = '/athena/elementolab/scratch/reference/igenomes' +} + +singularity { + enabled = true + envWhitelist='SINGULARITY_BINDPATH' + cacheDir = "/athena/elementolab/scratch/reference/.singularity/singularity_images_nextflow" + autoMounts = true +} + +process { + executor = 'slurm' + queue = 'panda_physbio' + scratch = true + scratch = '/scratchLocal/`whoami`_${SLURM_JOBID}' +} + +params { + max_memory = 32.GB + max_cpus = 8 + max_time = 24.h +} + From d630bcfb6c12f92a54907de7b821a60a6f218a97 Mon Sep 17 00:00:00 2001 From: Ashley S Doane Date: Thu, 11 Mar 2021 13:59:55 -0500 Subject: [PATCH 2/3] Create wcm.md --- docs/wcm.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 docs/wcm.md diff --git a/docs/wcm.md b/docs/wcm.md new file mode 100644 index 0000000..74918ac --- /dev/null +++ b/docs/wcm.md @@ -0,0 +1,24 @@ +# nf-core/configs: Weill Cornell Medicine Configuration + +All nf-core pipelines have been successfully configured for use on the panda cluster at the WCM. + +To use, run the pipeline with `-profile wcm`. This will download and launch the [`wcm.config`](../conf/wcm.config) which has been pre-configured with a setup suitable for the Pasteur 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. + +## Running the workflow on the Pasteur cluster + +Nextflow is not installed by default on the WCM cluster. + +- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) + +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 a login node but on a compute node or lab-specific interactive server when configured as a submit host. + +1. Run nextflow on a compute node or interactive server with submit host capability: + +```bash +# Run nextflow workflow +nextflow run \\ +nf-core/chipseq \\ +-resume \\ +-profile test,wcm +``` From 6343a7f87cbeaa24a81aa588998efefd0099ca57 Mon Sep 17 00:00:00 2001 From: Ashley S Doane Date: Thu, 11 Mar 2021 14:01:07 -0500 Subject: [PATCH 3/3] Update wcm.md --- docs/wcm.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/wcm.md b/docs/wcm.md index 74918ac..0785829 100644 --- a/docs/wcm.md +++ b/docs/wcm.md @@ -2,7 +2,7 @@ All nf-core pipelines have been successfully configured for use on the panda cluster at the WCM. -To use, run the pipeline with `-profile wcm`. This will download and launch the [`wcm.config`](../conf/wcm.config) which has been pre-configured with a setup suitable for the Pasteur 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. +To use, run the pipeline with `-profile wcm`. This will download and launch the [`wcm.config`](../conf/wcm.config) which has been pre-configured with a setup suitable for the WCM slurm 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. ## Running the workflow on the Pasteur cluster