#!/bin/bash -Ceuo pipefail
run_gatk_pileup_for_sample.py \
--bam Sig_18_Blood.recalibrated.bam \
--outfile Sig_18_Blood.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