.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_PON:BCFTOOLS_SORT (chip_pon)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/e55fbf89a25204b69caa404abcfd05/.command.sh
Size: 409 bytes
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_PON:BCFTOOLS_SORT (chip_pon)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools \
    sort \
    --output chip_pon.chip_pon.harmonized.vcf.gz \
    --temp-dir . \
    --output-type z --write-index=tbi \
    chip_pon.chip_pon.normalized.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_PON:BCFTOOLS_SORT":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS