The merge_fastq pipeline is already installed in legion. You just need to load nextflow and start using it:
module load blic-modules
module load nextflow
nextflow_mergefastq --inputdir DIR --outputdir DIRBy default, the pipeline runs with the legion configuration profile conf/legion.config if you submit it from legion, and with the myriad config conf/myriad.config if you send
the job from myriad.
The 'standard' configuration (using the local executor) is not enabled.