.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS (HCC1395_tumor_vs_HCC1395_BL)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/583808e97d523a9d89defdcef3d5b5/.command.sh
Size: 546 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
tabix HCC1395_tumor_vs_HCC1395_BL.tnseq.whatshap.chr21.phased.vcf.gz

bcftools concat \
    --output HCC1395_tumor_vs_HCC1395_BL.tnseq.whatshap.phased.vcf.gz \
    --allow-overlaps --output-type z --write-index=tbi \
    --threads 6 \
    HCC1395_tumor_vs_HCC1395_BL.tnseq.whatshap.chr21.phased.vcf.gz

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