#!/bin/bash -Ceuo pipefail
run_gatk_pileup_for_sample.py \
    --bam HCC1395_BL.recal.bam \
    --outfile HCC1395_BL.pileup.txt \
    --reference Homo_sapiens_assembly38.fasta \
    --genome GRCh38 \
     \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP":
    conpair: "$(run_gatk_pileup_for_sample.py --version 2>&1 | sed 's/.*version //' | sed 's/ .*//' || echo '1.0')"
    gatk: "$(gatk --version 2>&1 | grep 'GATK' | sed 's/.*GATK) v//' | sed 's/ .*//' || echo '4.6.2.0')"
    python: "$(python --version 2>&1 | sed 's/Python //' || echo '3.8.20')"
END_VERSIONS