#!/bin/bash -Ceuo pipefail
# Reconstruct the samples/{sample_id}/counts.tsv layout that cnv_pipe expects
for f in HG03391_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03391_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03578_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03578_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03259_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv HG03582_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv IHW09177_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03354_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03385_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03385_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03469_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03567_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03267_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03267_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03354_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03401_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv HG03461_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03461_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03469_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03567_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv IHW09161_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18877_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA18877_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv HG03259_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03259_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03401_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03446_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03582_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA12878_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA12878_c_0001_gDNA_0001_B23H2H2LT4_4_counts.tsv NA18877_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03202_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv HG03394_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03401_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03428_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03446_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03446_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv HG03449_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv IHW09133_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv NA12878_c_0001_gDNA_0001_B23H2H2LT4_5_counts.tsv NA18488_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18488_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA18523_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA18861_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18917_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18917_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03267_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv HG03394_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03428_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03485_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv HG03485_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv HG03449_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv IHW09191_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18520_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18520_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA18523_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18878_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18878_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv IHW09352_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv IHW09507_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv NA12878_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv NA12878_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA12878_c_0001_gDNA_0001_B23H2H2LT4_6_counts.tsv IHW09203_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv IHW09267_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv IHW09434_c_01_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18499_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA18861_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA19095_c_0001_gDNA_0001_B23H2H2LT4_2_counts.tsv NA19095_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA18499_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv NA19114_c_0001_gDNA_0001_B23H2H2LT4_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 \
         A237CFYLT3_1__sex_calls.parquet \
         A237CFYLT3_1__sex_calls.png \
         --max-workers 10