.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ (HCC1395_tumor_vs_HCC1395_BL:chr21)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/4e59882341fa7865f432f440dc1e3a/.command.sh
Size: 639 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ (HCC1395_tumor_vs_HCC1395_BL:chr21)
Attempt

Content

#!/bin/bash -Ceuo pipefail
if [ -n "chr21" ]; then
    tabix -h HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz chr21 > input_filtered.vcf
    bgzip input_filtered.vcf
    input_vcf="input_filtered.vcf.gz"
else
    input_vcf="HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz"
fi

whatshap \
    phase \
     \
    --reference Homo_sapiens_assembly38.fasta \
    -o HCC1395_tumor_vs_HCC1395_BL.tnseq.whatshap.chr21.phased.vcf.gz \
    $input_vcf \
    HCC1395_tumor.recalibrated.bam

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ":
    whatshap: $(whatshap --version)
END_VERSIONS