.command.sh - Workdir - DAQ:BAM_POSTDEDUP_QC:SAMTOOLS_STATS (13511611-cfDNA)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/408be319bd9181c70361182f855188/.command.sh
Size: 354 bytes
Task: DAQ:BAM_POSTDEDUP_QC:SAMTOOLS_STATS (13511611-cfDNA)
Attempt

Content

#!/bin/bash -Ceuo pipefail
samtools \
    stats \
    --threads 4 \
    --reference Homo_sapiens_assembly38.fasta \
     \
    13511611-cfDNA.md.bam \
    > 13511611-cfDNA.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