.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_GERMLINE:BCFTOOLS_NORM (HCC1395_BL)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/0cb7d4419b3e3df08da604229696bc/.command.sh
Size: 499 bytes
Task: NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:HARMONIZE_GERMLINE:BCFTOOLS_NORM (HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools norm \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output HCC1395_BL.germline.normalized.vcf.gz \
    -a -m -both --old-rec-tag OLD_VARIANT --output-type z --write-index=tbi \
    --threads 6 \
    HCC1395_BL.haplotyper_rf.gt_corrected.vcf.gz

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