nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow. Here we use Sarek workflow as an example pipeline to detect variants on whole genome or targeted sequencing data.
Here is an example batch script to run the pipeline on Puhti:
#!/bin/bash
#SBATCH --time=01:00:00
#SBATCH --partition=small
#SBATCH --account=project_xxxx
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4000
export SINGULARITY_TMPDIR=$PWD
export SINGULARITY_CACHEDIR=$PWD
unset XDG_RUNTIME_DIR
# Activate Nextflow on Puhti
module load nextflow
# nf-core pipeline examples here
# Variant calling on genome data
nextflow run nf-core/sarek -r 2.7.1 -profile test,singularity -resume
# proteomics example
# nextflow run nf-core/proteomicslfq -r 1.0.0 -profile test,singularity -resume
# metabolomics example
# nextflow run nf-core/metaboigniter -r 1.0.1 -profile test,singularity -resume
copy and paste the above script to a file named sarek_nfcore.sh and replace your project number with project_xxxx in slurm directives.
Finally, submit your job
sbatch sarek_nfcore.sh