#!/bin/bash -Ceuo pipefail
python /usr/local/bin/call_cnv.py \
    --tumor-parquet HCC1395_tumor_normalized.parquet \
    --normal-parquet HCC1395_BL_normalized.parquet \
    --pairs pairs.tsv \
    --specimen HCC1395_tumor_vs_HCC1395_BL \
    --output HCC1395_tumor_vs_HCC1395_BL_segments.tsv \
    --seg-output HCC1395_tumor_vs_HCC1395_BL.seg \
    --tumor-alleles HCC1395_tumor_alleles.tsv.gz \
    --normal-alleles HCC1395_BL_alleles.tsv.gz \
    --probe-agg-output HCC1395_tumor_vs_HCC1395_BL_probe_agg.tsv.gz \
    --plots-dir plots \
    --metrics-output HCC1395_tumor_vs_HCC1395_BL_metrics.tsv \
    --workers 4 \
     \
    --genome-annotations Homo_sapiens.GRCh38.110.chr21.gtf.gz \
    --gene-output HCC1395_tumor_vs_HCC1395_BL_gene_cnv.tsv \
    --vcf-output HCC1395_tumor_vs_HCC1395_BL_somatic.vcf \
    --fit-method clonal-decomp --mode ascn

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_CALL":
    soma-cnv: 20260604-3cb5ec5
END_VERSIONS