.command.sh - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDUPLICATION (tih_rna_sample_00088_23H5VFLT4_s02)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/74aa4ec924bcb52bfd16642b2f279c/.command.sh
Size: 440 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_READDUPLICATION (tih_rna_sample_00088_23H5VFLT4_s02)
Attempt

Content

#!/bin/bash -euo pipefail
read_duplication.py \
    -i tih_rna_sample_00088_23H5VFLT4_s02.Aligned.sortedByCoord.out.bam tih_rna_sample_00088_23H5VFLT4_s02.Aligned.sortedByCoord.out.bam.bai \
    -o tih_rna_sample_00088_23H5VFLT4_s02 \


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