.command.sh - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM (1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/0e84f931a9d392188e7e496ef83f94/.command.sh
Size: 517 bytes
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM (1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
if true
then
    for VCFGZ in *.vcf.gz; do
        gunzip -cdf $VCFGZ > $( basename $VCFGZ .gz );
    done
fi

NCM_REF="./"Homo_sapiens_assembly38.fasta ncm.py -d . -bed SNP_GRCh38_hg38_wChr.bed -O . -N ngscheckmate -V

if true
then
    rm -f *.vcf  # clean up decompressed vcfs
fi

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM":
    ngscheckmate: $(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
END_VERSIONS