#!/bin/bash -Ceuo pipefail
estimate_tumor_normal_contamination.py \
    -T HCC1395_tumor.pileup.txt \
    -N HCC1395_BL.pileup.txt \
    -g GRCh38 \
     \
    --outfile HCC1395_tumor_vs_HCC1395_BL.conpair.contamination.txt \
    --grid 0.01 \
    --min_mapping_quality 10 \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_CONTAMINATION_ANALYSIS:CONPAIR_CONTAMINATION":
    conpair: "$(estimate_tumor_normal_contamination.py --version 2>&1 | sed 's/.*version //' | sed 's/ .*//' || echo '1.0')"
    python: "$(python --version 2>&1 | sed 's/Python //' || echo '3.8.20')"
    numpy: "$(python -c 'import numpy; print(numpy.__version__)' 2>/dev/null || echo '1.24.4')"
END_VERSIONS