.command.sh - Workdir - NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (seracare_75pct_rep2;manta)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/8971143622fd54a6378eb0355dcc6d/.command.sh
Size: 390 bytes
Task: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (seracare_75pct_rep2;manta)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools stats \
     \
     \
     \
     \
     \
     \
    seracare_75pct_rep2.manta.somatic_sv.vcf.gz > seracare_75pct_rep2.manta.somatic_sv.bcftools_stats.txt

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