nxf.txt

# step 0. load required modules
module load nextflow/22.10.1

# step 1: transfer data using HTTPS + curl
# (assume transfer.sh is on PATH)
transfer.sh {work_dir}

# step 2. run pgsc_calc!
nextflow run pgscatalog/pgsc_calc -profile test,singularity \
         -c {work_dir}/{name}/config \
         -c {work_dir}/{name}/allas.config \
         --input {work_dir}/{name}/input.json \
         --min_overlap 0.01 \
         --max_cpus 40 \
         --max_memory "32.GB" \
         --parallel