.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT (NA12878_c_0002_gDNA_0005_B23KYWJLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/e54d846ece59ee7281d0612a586e6f/.command.sh
Size: 466 bytes
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_CHIP_CANDIDATES:BCFTOOLS_SORT (NA12878_c_0002_gDNA_0005_B23KYWJLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools \
    sort \
    --output NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.chip.harmonized.vcf.gz \
    --temp-dir . \
    --output-type z --write-index=tbi \
    NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.chip.normalized.vcf.gz

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