.command.sh - Workdir - DAQ:AGGREGATE_POSTDEDUP_QC (postdedup_qc_aggregation)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/92efc9d4a2fa974fff4050983b0324/.command.sh
Size: 242.4 KB
Task: DAQ:AGGREGATE_POSTDEDUP_QC (postdedup_qc_aggregation)
Attempt
Content

#!/bin/bash -Ceuo pipefail
# Write manifest JSON file
    cat << 'EOF' > manifest.json
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["1136_7OW-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1173_JXL-N1-BDNA-01_B23KGCJLT4_1",["1173_JXL-N1-BDNA-01_B23KGCJLT4_1_full_basic_stats.tsv"],"659_cVw-N1-BDNA-1_B23KGCJLT4_1",["659_cVw-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_6DX-N1-BDNA-1_B23KGCJLT4_1",["1136_6DX-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_6G2-N1-BDNA-1_B23KGCJLT4_1",["1136_6G2-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_6J4-N1-BDNA-1_B23KGCJLT4_1",["1136_6J4-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_BF84-N1-BDNA-1_B23KGCJLT4_1",["1029_BF84-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_85T-N1-BDNA-1_B23KGCJLT4_1",["1136_85T-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_2LG-N1-BDNA-1_B23KGCJLT4_1",["1136_2LG-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_5OE-N1-BDNA-1_B23KGCJLT4_1",["1136_5OE-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_I7E-N1-BDNA-1_B23KGCJLT4_1",["1029_I7E-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1047_BE-N1-BDNA-1_B23KGCJLT4_1",["1047_BE-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_1EO-N1-BDNA-1_B23KGCJLT4_1",["1136_1EO-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_cAa-N1-BDNA-1_B23KGCJLT4_1",["659_cAa-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1047_5-N1-BDNA-1_B23KGCJLT4_1",["1047_5-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_BAE3-N1-BDNA-1_B23KGCJLT4_1",["1029_BAE3-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_55O-N1-BDNA-1_B23KGCJLT4_1",["1136_55O-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_4C4-N1-BDNA-1_B23KGCJLT4_1",["1136_4C4-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_HOD-N1-BDNA-1_B23KGCJLT4_1",["1029_HOD-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_BLBE-N1-BDNA-1_B23KGCJLT4_1",["1029_BLBE-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_FVW-N1-BDNA-1_B23KGCJLT4_1",["1029_FVW-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_R1-N1-BDNA-1_B23KGCJLT4_1",["659_R1-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_6D4-N1-BDNA-1_B23KGCJLT4_1",["1136_6D4-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_65P-N1-BDNA-1_B23KGCJLT4_1",["1136_65P-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_bhK-N1-BDNA-1_B23KGCJLT4_1",["659_bhK-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_3MV-N1-BDNA-1_B23KGCJLT4_1",["1136_3MV-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_00H-N1-BDNA-1_B23KGCJLT4_1",["1136_00H-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_IWL-N1-BDNA-1_B23KGCJLT4_1",["1029_IWL-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_8B-N1-BDNA-1_B23KGCJLT4_1",["1136_8B-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_5Q-N1-BDNA-1_B23KGCJLT4_1",["1136_5Q-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_bTq-N1-BDNA-1_B23KGCJLT4_1",["659_bTq-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_253-N1-BDNA-1_B23KGCJLT4_1",["1136_253-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_8F1-N1-BDNA-1_B23KGCJLT4_1",["1136_8F1-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_42A-N1-BDNA-1_B23KGCJLT4_1",["1136_42A-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_7NX-N1-BDNA-1_B23KGCJLT4_1",["1136_7NX-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_81M-N1-BDNA-1_B23KGCJLT4_1",["1136_81M-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_6BL-N1-BDNA-1_B23KGCJLT4_1",["1136_6BL-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_5AC-N1-BDNA-1_B23KGCJLT4_1",["1136_5AC-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_bgw-N1-BDNA-1_B23KGCJLT4_1",["659_bgw-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_4ZB-N1-BDNA-1_B23KGCJLT4_1",["1136_4ZB-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_5PU-N1-BDNA-1_B23KGCJLT4_1",["1136_5PU-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_egp-N1-BDNA-1_B23KGCJLT4_1",["659_egp-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_1BK-N1-BDNA-1_B23KGCJLT4_1",["1029_1BK-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_BICJ-N1-BDNA-1_B23KGCJLT4_1",["1029_BICJ-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_4VJ-N1-BDNA-1_B23KGCJLT4_1",["1136_4VJ-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_djb-N1-BDNA-2_B23KGCJLT4_1",["659_djb-N1-BDNA-2_B23KGCJLT4_1_full_basic_stats.tsv"],"659_dm4-N1-BDNA-1_B23KGCJLT4_1",["659_dm4-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_50G-N1-BDNA-1_B23KGCJLT4_1",["1136_50G-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_4VB-N1-BDNA-1_B23KGCJLT4_1",["1136_4VB-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_dHy-N1-BDNA-1_B23KGCJLT4_1",["659_dHy-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_16G-N1-BDNA-1_B23KGCJLT4_1",["1029_16G-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"NA12878_c_0002_gDNA_0002_B23KGCJLT4_1",["NA12878_c_0002_gDNA_0002_B23KGCJLT4_1_full_basic_stats.tsv"],"659_bR4-N1-BDNA-1_B23KGCJLT4_1",["659_bR4-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_491-N1-BDNA-1_B23KGCJLT4_1",["1136_491-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_GF2-N1-BDNA-1_B23KGCJLT4_1",["1029_GF2-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_27F-N1-BDNA-1_B23KGCJLT4_1",["1136_27F-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_eKx-N1-BDNA-1_B23KGCJLT4_1",["659_eKx-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_buj-N1-BDNA-1_B23KGCJLT4_1",["659_buj-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_11H-N1-BDNA-1_B23KGCJLT4_1",["1029_11H-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"NA12878_c_0002_gDNA_0001_B23KGCJLT4_1",["NA12878_c_0002_gDNA_0001_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_F0L-N1-BDNA-1_B23KGCJLT4_1",["1029_F0L-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_63V-N1-BDNA-1_B23KGCJLT4_1",["1136_63V-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_67D-N1-BDNA-1_B23KGCJLT4_1",["1136_67D-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_4XR-N1-BDNA-1_B23KGCJLT4_1",["1136_4XR-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_eZ4-N1-BDNA-1_B23KGCJLT4_1",["659_eZ4-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_01S-N1-BDNA-1_B23KGCJLT4_1",["1029_01S-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_BMFL-N1-BDNA-1_B23KGCJLT4_1",["1029_BMFL-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_FZO-N1-BDNA-1_B23KGCJLT4_1",["1029_FZO-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_e0S-N1-BDNA-1_B23KGCJLT4_1",["659_e0S-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_49M-N1-BDNA-1_B23KGCJLT4_1",["1136_49M-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_5JK-N1-BDNA-1_B23KGCJLT4_1",["1136_5JK-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1",["1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"1136_5ZG-N1-BDNA-1_B23KGCJLT4_1",["1136_5ZG-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_bQZ-N1-BDNA-1_B23KGCJLT4_1",["659_bQZ-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_rd-N1-BDNA-1_B23KGCJLT4_1",["659_rd-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_Fr-N1-BDNA-1_B23KGCJLT4_1",["659_Fr-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"],"659_mK-N1-BDNA-1_B23KGCJLT4_1",["659_mK-N1-BDNA-1_B23KGCJLT4_1_full_basic_stats.tsv"]]}
EOF

    cat << 'EOF' > panel_mapping.json
{"xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed":"all_targets","xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed":"all_probes","altera_v3_targets_postQC_hg38.bed":"boosted_depth","altera_v3_targets_coding_postQC_hg38.bed":"coding_depth","altera_v3_targets_noncoding_postQC_hg38.bed":"noncoding_depth","xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed":"non_boosted_depth","FINAL_hotspot_list_07302025_hg38_sorted.bed":"hotspot_depth","foresight_clarity_targets_hg38.bed":"foresight_depth"}
EOF

    # Run aggregation script (outputs single JSON)
    aggregate_qc_metrics.py \
        --mode postdedup \
        --manifest manifest.json \
        --panel-mapping panel_mapping.json \
        --files-dir . \
        --output postdedup_qc.json \
        --no-summary

cat <<-END_VERSIONS > versions.yml
"DAQ:AGGREGATE_POSTDEDUP_QC":
    python: $(python --version | sed 's/Python //g')
    aggregate_qc_metrics: 1.0.0
END_VERSIONS