.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDISTRIBUTION (BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/95286180c1a0351c274a2247e7af23/.command.sh
Size: 494 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDISTRIBUTION (BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
read_distribution.py \
    -i BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    > BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.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