The Sarek pipeline is already installed in legion and myriad. You just need to load nextflow and start using it:
module load blic-modules
module load nextflow
nextflow run /shared/ucl/depts/cancer/apps/nextflow_pipelines/Sarek/main.nf -profile --sample input_somatic.tsv --genome GRCh38 You need to specify an appropiate configuration profile with the -profile argument. Please use the legion configuration profile conf/legion.config if you submit it from
legion, and the myriad config conf/myriad.config if you send the job from myriad.