.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA (dna_s771)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/e2a7bb3b79015b8e2e2bea03d39d9d/.command.sh
Size: 544 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA (dna_s771)
Attempt

Content

#!/bin/bash -euo pipefail
arriba \
    -x dna_s771.Aligned.sortedByCoord.out.bam \
    -a ref_genome.fa \
    -g ref_annot.gtf \
    -o dna_s771.arriba.fusions.tsv \
    -O dna_s771.arriba.fusions.discarded.tsv \
    -b blacklist_hg38_GRCh38_v2.4.0.tsv.gz \
    -k known_fusions_hg38_GRCh38_v2.4.0.tsv.gz \
     \
     \
    -p protein_domains_hg38_GRCh38_v2.4.0.gff3 \


cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA":
    arriba: $(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version: //')
END_VERSIONS