nf-core
nf-core is an international community effort to collect a curated set of analysis pipelines built using Nextflow.
Before starting to write your own NGS pipeline, head to the nf-core website and check if somebody else didn’t write it already. Moreover, if the solution provided by nf-core missing some things for your need you can build up from the available pipeline instead of writing everything from scratch.
PSMN
Setting up your environment
To use an nf-core pipeline on the PSMN you first need to set up a few things:
Add the following line in your ~/.bashrc
or ~/.zshrc
file:
2023/06/26 edit add the -b /home
for the charliecloud update
PATH=/Xnfs/abc/charliecloud_bin/:/Xnfs/abc/nextflow_bin:$PATH
This will add the nextflow and charliecloud binaries to your PATH
and create a shortcut to use the last nf-core tools image with charliecloud.
Downloading an nf-core pipeline
You can use the following command to download any nf-core pipeline for this list.
The following example uses the rnaseq
pipeline. You need to replace the <user_name>
with your PSMN login.
ch-run -b /scratch:/scratch -b /Xnfs -b /home -c $(pwd) /Xnfs/abc/charliecloud/img/nfcore%tools+2.6 -- \
-r 3.8.1 --outdir /scratch/Bio/<user_name>/nf-core-rnaseq -x none -c none nf-core download rnaseq
With :
rnaseq
the name of the pipeline3.8.1
the version of the pipeline/scratch/Bio/<user_name>/nf-core-rnaseq
the absolute path of the folder where to save the pipeline
If this is the first time that this pipeline is launched at the PSMN you then need to download the charliecloud containers corresponding to this pipeline.
cd /scratch/Bio/<user_name>/nf-core-rnaseq/
pull_ch_images.sh
You may encounter Permission denied
errors when running the pull_ch_images.sh
scripts. You can bypass this problem by downloading charliecloud containers inside your home directory (folder ~/charliecloud_storage/
) and move them in the shared location (/Xnfs/abc/charliecloud/
). To do that run:
cd /scratch/Bio/<user_name>/nf-core-rnaseq/
pull_ch_images_locally.sh
Running an nf-core pipeline on the PSMN
You can use a combination of the test
and psmn
profile to test your pipeline on the PSMN:
cd /scratch/Bio/<user_name>/nf-core-rnaseq/
nextflow run workflow -profile test,psmn --outdir results_test
If everything works, you can head to your pipeline documentation and only keep the -profile psmn
to run your pipeline on the PSMN.