#!/bin/bash -Ceuo pipefail
# Reconstruct the samples/{sample_id}/counts.tsv layout that cnv_pipe expects
for f in NTC_0001_0001_B23H2GYLT3_1_counts.tsv NTC_0002_0001_A23MHW3LT4_1_counts.tsv NTC_0001_0001_A23H3W5LT3_1_counts.tsv NTC_0001_0001_A23H3W5LT3_2_counts.tsv NTC_0002_0001_A23MHW3LT4_2_counts.tsv NTC_0002_0002_A23MHW3LT4_1_counts.tsv NTC_0002_0047_A23MHW3LT4_1_counts.tsv 1173_NMN-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1029_I2Q-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_DQI-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_0EH-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_2BI-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_0UA-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_67V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1029_26C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BPC3-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_M9U-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_0JP-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0NH-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_7FA-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_BKJD-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BNY-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_13-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_84H-N1-BDNA-1_A23MHW3LT4_1_counts.tsv NA12878_c_0002_gDNA_0007_A23MHW3LT4_1_counts.tsv 1029_1UX-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_22Q-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_344-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BLVT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BNM7-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_D19-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GWX-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_KET-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_KR2-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_1UN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_1EQ-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0PG-N1-BDNA-1_A23H3W5LT3_1_counts.tsv NA08618_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv 1136_20M-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_22N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_26U-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2DN-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1173_CRL-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1173_NWE-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1029_1CZ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_4X0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_DB2-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_MH0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_OHN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_ROB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_YHI-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_10H-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_0T4-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_35Z-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_3T8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4DY-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4VV-N1-BDNA-1_A23H3W5LT3_1_counts.tsv HG03694_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA01359_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA12878_c_0003_gDNA_0002_A23H3W5LT3_1_counts.tsv 1136_229-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_24Z-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_251-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_25V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_26N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_282-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1173_JLC-N1-BDNA-01_A23MHW3LT4_1_counts.tsv 1029_7AL-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BF1C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BNMN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BQ3K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BTW1-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_C3S-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_JJU-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_P0W-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_Q3K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_RCF-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_47X-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4HC-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_6C2-N1-BDNA-1_A23H3W5LT3_1_counts.tsv NA07106_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA07891_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA12074_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA14626_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv 1136_200-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_29V-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2AR-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2CZ-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1029_BI3C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BMDN-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BOCP-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BQ0K-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GP0-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_LNB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_NHT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_1V8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_5W-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_7F8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_8EX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv HG00259_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG02977_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG02982_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA11570_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv 1136_23E-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_250-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2C0-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2HR-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1173_PCB-N1-BDNA-02_A23MHW3LT4_1_counts.tsv 1029_3PB-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_B1C-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BCTD-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BDK5-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_G7F-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GNJ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_19H-N1-BDNA-1_B23H2GYLT3_1_counts.tsv NA12878_c_0003_gDNA_0002_B23H2GYLT3_1_counts.tsv 1136_02S-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_5FD-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_8FN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv HG00634_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG02878_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG03267_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA01535_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA03184_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA13451_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA20539_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv 1136_25E-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1173_9C-N1-BDNA-01_A23MHW3LT4_1_counts.tsv NA12878_c_0002_gDNA_0008_A23MHW3LT4_1_counts.tsv 1029_BC9J-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BL7I-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_GG5-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_NXR-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_2HX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4SO-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_5CN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv HG00187_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG03259_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA03226_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA07081_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv NA14234_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv 1136_209-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_211-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2B2-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2GE-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1173_J3R-N1-BDNA-01_A23MHW3LT4_1_counts.tsv NA12878_c_0002_gDNA_0001_A23MHW3LT4_1_counts.tsv 1029_7OE-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_0YQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_24I-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_4HJ-N1-BDNA-1_A23H3W5LT3_1_counts.tsv HG02111_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA12878_c_0003_gDNA_0002_A23H3W5LT3_2_counts.tsv 1136_20J-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_2FA-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1029_BBPA-N1-BDNA-1_B23H2GYLT3_1_counts.tsv HG01242_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv HG03857_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv NA19404_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv 1136_20N-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_04F-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_0W-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_25Q-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_3K7-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_7EX-N1-BDNA-1_A23H3W5LT3_1_counts.tsv NA12606_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv 1029_3HC-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BGPR-N1-BDNA-1_B23H2GYLT3_1_counts.tsv HG00731_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv 1136_2FY-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1029_W1O-N1-BDNA-1_B23H2GYLT3_1_counts.tsv NA12878_c_0002_gDNA_0002_A23MHW3LT4_1_counts.tsv 1029_NMM-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_R8U-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_2GM-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_0B-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_203-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1136_03N-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1136_2FO-N1-BDNA-1_A23MHW3LT4_1_counts.tsv 1029_BO4N-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_UCZ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_BON7-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_UKQ-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_V13-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_W7S-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_WTT-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_MB8-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1029_CWN-N1-BDNA-1_A23H3W5LT3_1_counts.tsv 1136_024-N1-BDNA-1_B23H2GYLT3_1_counts.tsv 1029_XPW-N1-BDNA-1_B23H2GYLT3_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 \
         A23TY32LT4_1__sex_calls.parquet \
         A23TY32LT4_1__sex_calls.png \
         --max-workers 10