.command.sh - Workdir - DAQ:BAM_POSTDEDUP_QC:SAMTOOLS_STATS (1136_3LU-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/8fc33c1860a9a195bb4d539ef45510/.command.sh
Size: 388 bytes
Task: DAQ:BAM_POSTDEDUP_QC:SAMTOOLS_STATS (1136_3LU-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
samtools \
    stats \
    --threads 4 \
    --reference Homo_sapiens_assembly38.fasta \
     \
    1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam \
    > 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.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