#!/bin/bash -Ceuo pipefail
python /usr/local/bin/call_cnv.py \
    --tumor-parquet Sig_18_tissue_normalized.parquet \
    --normal-parquet Sig_18_Blood_normalized.parquet \
    --pairs pairs.tsv \
    --specimen custom_Sig_18_tumor_normal \
    --output custom_Sig_18_tumor_normal_segments.tsv \
    --seg-output custom_Sig_18_tumor_normal.seg \
    --tumor-alleles Sig_18_tissue_alleles.tsv.gz \
    --normal-alleles Sig_18_Blood_alleles.tsv.gz \
    --probe-agg-output custom_Sig_18_tumor_normal_probe_agg.tsv.gz \
    --plots-dir plots \
    --metrics-output custom_Sig_18_tumor_normal_metrics.tsv \
    --workers 4 \
     \
    --genome-annotations Homo_sapiens.GRCh38.110.chr21.gtf.gz \
    --gene-output custom_Sig_18_tumor_normal_gene_cnv.tsv \
    --vcf-output custom_Sig_18_tumor_normal_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