.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDISTRIBUTION (rna_s1221_S42)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/83b6edf145d03938c66e5aa42eaa71/.command.sh
Size: 422 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDISTRIBUTION (rna_s1221_S42)
Attempt

Content

#!/bin/bash -euo pipefail
read_distribution.py \
    -i rna_s1221_S42.Aligned.sortedByCoord.out.bam rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    > rna_s1221_S42.read_distribution.txt

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