File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/9d622f662c274f913960f1d5fd920d/.command.sh
Size
636 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:WHATSHAP_TNSEQ (custom_Sig_18_tumor_normal:chr21)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
if [ -n "chr21" ]; then
    tabix -h custom_Sig_18_tumor_normal.tnseq.filtered.vcf.gz chr21 > input_filtered.vcf
    bgzip input_filtered.vcf
    input_vcf="input_filtered.vcf.gz"
else
    input_vcf="custom_Sig_18_tumor_normal.tnseq.filtered.vcf.gz"
fi

whatshap \
    phase \
     \
    --reference Homo_sapiens_assembly38.fasta \
    -o custom_Sig_18_tumor_normal.tnseq.whatshap.chr21.phased.vcf.gz \
    $input_vcf \
    Sig_18_tissue.recalibrated.bam

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