.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (dna_s761)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/e0b7d006637bfd34fd15c5fc95e827/.command.sh
Size: 487 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (dna_s761)
Attempt

Content

#!/bin/bash -euo pipefail
junction_annotation.py \
    -i dna_s761.Aligned.sortedByCoord.out.bam dna_s761.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o dna_s761 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee dna_s761.junction_annotation.log >&2)

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION":
    rseqc: $(junction_annotation.py --version | sed -e "s/junction_annotation.py //g")
END_VERSIONS