.command.sh - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS (1029_11H-N1-BDNA-1_B23KGCJLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/e00fa0684708c9e2b6200410e8840c/.command.sh
Size: 425 bytes
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS (1029_11H-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
samtools \
    stats \
    --threads 1 \
    --reference Homo_sapiens_assembly38.fasta \
    1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam \
    > 1029_11H-N1-BDNA-1_B23KGCJLT4_1.stats

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