#!/bin/bash -Ceuo pipefail
# Reconstruct the samples/{sample_id}/counts.tsv layout that cnv_pipe expects
for f in 1029_2LI-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BNG8-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_0DT-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_3OH-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_5IX-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BSZ8-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_FOO-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_FR4-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_05O-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_0NX-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_3N0-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_4J3-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BF2U-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BPLF-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_FWL-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_GW0-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_032-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_1H5-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_1G0-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_2IN-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_4Z2-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_56D-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_7Y1-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BCTO-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BOHJ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BQMQ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_DOC-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_E36-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_8OI-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BA0-N2-BDNA-1_235YY7LT3_1_counts.tsv 1029_BCB6-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BIHC-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BO4Y-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BOSD-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BP21-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BQXQ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BRTT-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BS78-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BSOQ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_EDH-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_EFW-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_EM-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_FXQ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_G5I-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_G94-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_5O3-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BBOC-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BBCQ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BG5-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BGMF-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BK2H-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BLU1-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BQKE-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_DV0-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_EMM-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_8AV-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_8BO-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BDOZ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BFKM-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BGFD-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BJH0-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BLH5-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BN9Y-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BQD7-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BSWE-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_C35-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_FBB-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_GGQ-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_GS7-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BBS1-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BICA-N1-BDNA-1_235YY7LT3_1_counts.tsv 1029_BIHO-N1-BDNA-1_235YY7LT3_1_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 \
         A23H3NYLT3_1__sex_calls.parquet \
         A23H3NYLT3_1__sex_calls.png \
         --max-workers 10