#!/bin/bash -Ceuo pipefail
python /usr/local/bin/call_cnv.py \
    --tumor-parquet 1029_0I-T1-TDNA-1_A23KCGYLT4_1_normalized.parquet \
    --normal-parquet 1029_0I-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet \
    --pairs pairs.tsv \
    --specimen 1029_0I \
    --output 1029_0I_segments.tsv \
    --seg-output 1029_0I.seg \
    --tumor-alleles 1029_0I-T1-TDNA-1_A23KCGYLT4_1_alleles.tsv.gz \
    --normal-alleles 1029_0I-N1-BDNA-1_B23KGCJLT4_1_alleles.tsv.gz \
    --probe-agg-output 1029_0I_probe_agg.tsv.gz \
    --plots-dir plots \
    --metrics-output 1029_0I_metrics.tsv \
    --workers 4 \
     \
    --genome-annotations Homo_sapiens.GRCh38.110.gtf.gz \
    --gene-output 1029_0I_gene_cnv.tsv \
    --vcf-output 1029_0I_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: 20260603-050173b
END_VERSIONS