#!/bin/bash -Ceuo pipefail
# Reconstruct the samples/{sample_id}/counts.tsv layout that cnv_pipe expects
for f in 1136_676-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_617-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6V6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7XB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_823-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6ED-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6LJ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6WG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7SE-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6GU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_66D-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6QH-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6TD-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_75R-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_75S-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7NZ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7PX-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7Z4-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_874-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_5Q6-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_62I-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6KP-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6LT-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6XF-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_72X-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_77B-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_87H-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 659_b4x-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_61N-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_72N-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_74W-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_63A-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_65T-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6QL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6SE-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6ZL-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7TS-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4BI-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4KD-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_5WB-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4CH-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_89H-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4M9-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_665-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_6HR-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7DO-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7PV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7Y3-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_8DK-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4IN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4KR-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7H5-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7VC-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_8A3-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_8CD-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 659_6i-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4QQ-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_57L-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_5FY-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7EK-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_8-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4DU-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4FG-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4QC-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_5MS-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_5SV-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4II-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_52W-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_5TR-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_4A2-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_5NN-N1-BDNA-1_B23KFG5LT4_1_counts.tsv 1136_7IK-N1-BDNA-1_B23KFG5LT4_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 \
         B237YJMLT3_1__sex_calls.parquet \
         B237YJMLT3_1__sex_calls.png \
         --max-workers 10