File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/e211cac2da80f06c1ca61f70de9445/.command.sh
Size
622 bytes
Task
NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA (ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1)
Attempt

Content

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#!/bin/bash -euo pipefail
arriba \
    -x ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam \
    -a ref_genome.fa \
    -g ref_annot.gtf \
    -o ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv \
    -O ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.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