.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDUPLICATION (BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/9c1caa17e7f65a1e76938f434893e0/.command.sh
Size: 449 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDUPLICATION (BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
read_duplication.py \
    -i BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -o BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1 \


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