.command.sh - Workdir - DAQ:BAM_POSTDEDUP_QC:SAMTOOLS_STATS (T21-D0003322)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/fcbf75a6c18805c0955a2f6143f635/.command.sh
Size: 350 bytes
Task: DAQ:BAM_POSTDEDUP_QC:SAMTOOLS_STATS (T21-D0003322)
Attempt

Content

#!/bin/bash -Ceuo pipefail
samtools \
    stats \
    --threads 4 \
    --reference Homo_sapiens_assembly38.fasta \
     \
    T21-D0003322.md.bam \
    > T21-D0003322.stats

cat <<-END_VERSIONS > versions.yml
"DAQ:BAM_POSTDEDUP_QC:SAMTOOLS_STATS":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS