File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/e4c5160390f9ef7c3e0f1caff546ac/.command.sh
Size
4.5 KB
Task
NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (PatientB_tumor_vs_PatientB_normal;strelka)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.vcf
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.bcf
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.frq
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.frq.count
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.idepth
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.ldepth
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.ldepth.mean
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.gdepth
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.hap.ld
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.geno.ld
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.geno.chisq
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.list.hap.ld
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.list.geno.ld
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.interchrom.hap.ld
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.interchrom.geno.ld
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.TsTv
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.TsTv.summary
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.TsTv.count
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.TsTv.qual
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.FILTER.summary
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.sites.pi
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.windowed.pi
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.weir.fst
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.het
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.hwe
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.Tajima.D
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.ifreqburden
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.LROH
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.relatedness
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.relatedness2
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.lqual
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.imiss
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.lmiss
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.snpden
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.kept.sites
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.removed.sites
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.singletons
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.indel.hist
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.hapcount
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.mendel
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.FORMAT
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.INFO
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.012
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.012.indv
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.012.pos
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.impute.hap
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.impute.hap.legend
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.impute.hap.indv
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.ldhat.sites
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.ldhat.locs
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.BEAGLE.GL
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.BEAGLE.PL
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.ped
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.map
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.tped
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.tfam
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.diff.sites_in_files
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.diff.indv_in_files
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.diff.sites
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.diff.indv
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.diff.discordance.matrix
touch PatientB_tumor_vs_PatientB_normal.strelka.somatic_snvs.diff.switch

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