#!/bin/bash -Ceuo pipefail
# Reconstruct the samples/{sample_id}/counts.tsv layout that cnv_pipe expects
for f in Sig_18_tissue_counts.tsv Sig_18_Blood_counts.tsv HCC1395_tumor_counts.tsv HCC1395_BL_counts.tsv; do
    sample_id=$(basename "$f" _counts.tsv)
    mkdir -p "samples/${sample_id}"
    ln -s "$(pwd)/$f" "samples/${sample_id}/counts.tsv"
done

cnv_pipe process-batch \
         germline_cnv_input.csv \
         altera_v3_panel.bed \
         altera_v3_variable_regions.bed \
         $(pwd) \
         counts_1.parquet \
         sample_metrics_1.parquet \
         ploidy_1.parquet \
         REGRESSION_1__sex_calls.parquet \
         REGRESSION_1__sex_calls.png \
         --max-workers 10