File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/4d36dc316d3446fccccad1cfd688f8/.command.sh
Size
476 bytes
Task
NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (1029_01F-T1-TDNA-1_B23VCL7LT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1;strelka)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
vcftools \
    --gzvcf 1029_01F-T1-TDNA-1_B23VCL7LT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs.vcf.gz \
    --out 1029_01F-T1-TDNA-1_B23VCL7LT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.strelka.somatic_snvs \
    --TsTv-by-count \
     \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT":
    vcftools: $(echo $(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
END_VERSIONS