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

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/4d137667d7ea1637ffe2d0ad02cc15/.command.sh
Size: 449 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDUPLICATION (BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1)
Attempt

Content

#!/bin/bash -euo pipefail
read_duplication.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 \
    -o BreastNB_FFPE_L01_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