.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS (custom_Sig_18_tumor_normal)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/f0297e26822570731fc479656d2c29/.command.sh
Size: 543 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:CONCAT_WHATSHAP_TNSEQ_VCFS (custom_Sig_18_tumor_normal)
Attempt

Content

#!/bin/bash -Ceuo pipefail
tabix custom_Sig_18_tumor_normal.tnseq.whatshap.chr21.phased.vcf.gz

bcftools concat \
    --output custom_Sig_18_tumor_normal.tnseq.whatshap.phased.vcf.gz \
    --allow-overlaps --output-type z --write-index=tbi \
    --threads 6 \
    custom_Sig_18_tumor_normal.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