File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/c28811a5afdc0b28b5989599c69f9a/.command.sh
Size
469.7 KB
Task
NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
cat << 'EOF' > manifest.json
{"pairs":[{"pair_id":"1029_01S-T1-TDNA-1_B23KFCWLT4_1_vs_1029_01S-N1-BDNA-1_B23KGCJLT4_1","tumor_sample":"1029_01S-T1-TDNA-1_B23KFCWLT4_1","normal_sample":"1029_01S-N1-BDNA-1_B23KGCJLT4_1"},{"pair_id":"1029_05O-T1-TDNA-1_23FC2GLT4_s02_vs_1029_05O-N1-BDNA-1_2375WFLT3_s02","tumor_sample":"1029_05O-T1-TDNA-1_23FC2GLT4_s02","normal_sample":"1029_05O-N1-BDNA-1_2375WFLT3_s02"},{"pair_id":"1029_05O-T1-TDNA-1_23K7YCLT4_1_vs_1029_05O-N1-BDNA-1_235YY7LT3_1","tumor_sample":"1029_05O-T1-TDNA-1_23K7YCLT4_1","normal_sample":"1029_05O-N1-BDNA-1_235YY7LT3_1"},{"pair_id":"1029_0W2-T1-TDNA-1_A23KCGYLT4_1_vs_1029_0W2-N1-BDNA-1_B23KGCJLT4_1","tumor_sample":"1029_0W2-T1-TDNA-1_A23KCGYLT4_1","normal_sample":"1029_0W2-N1-BDNA-1_B23KGCJLT4_1"},{"pair_id":"1029_0W2-T1-TDNA-1_A23TNLVLT4_1_vs_1029_0W2-N1-BDNA-1_B23KGCJLT4_1","tumor_sample":"1029_0W2-T1-TDNA-1_A23TNLVLT4_1","normal_sample":"1029_0W2-N1-BDNA-1_B23KGCJLT4_1"},{"pair_id":"1029_0W2-T1-TDNA-1_B23NN7CLT4_1_vs_1029_0W2-N1-BDNA-1_B23KGCJLT4_1","tumor_sample":"1029_0W2-T1-TDNA-1_B23NN7CLT4_1","normal_sample":"1029_0W2-N1-BDNA-1_B23KGCJLT4_1"},{"pair_id":"1029_16G-T1-TDNA-1_B23KFCWLT4_1_vs_1029_16G-N1-BDNA-1_B23KGCJLT4_1","tumor_sample":"1029_16G-T1-TDNA-1_B23KFCWLT4_1","normal_sample":"1029_16G-N1-BDNA-1_B23KGCJLT4_1"},{"pair_id":"1029_22Q-T1-TDNA-1_A23NYHCLT4_1_vs_1029_22Q-N1-BDNA-1_B23H2GYLT3_1","tumor_sample":"1029_22Q-T1-TDNA-1_A23NYHCLT4_1","normal_sample":"1029_22Q-N1-BDNA-1_B23H2GYLT3_1"},{"pair_id":"1029_2IN-T1-TDNA-1_23FC2GLT4_s07_vs_1029_2IN-N1-BDNA-1_2375WFLT3_s07","tumor_sample":"1029_2IN-T1-TDNA-1_23FC2GLT4_s07","normal_sample":"1029_2IN-N1-BDNA-1_2375WFLT3_s07"},{"pair_id":"1029_2IN-T1-TDNA-1_23K7YCLT4_1_vs_1029_2IN-N1-BDNA-1_235YY7LT3_1","tumor_sample":"1029_2IN-T1-TDNA-1_23K7YCLT4_1","normal_sample":"1029_2IN-N1-BDNA-1_235YY7LT3_1"},{"pair_id":"1029_2PG-T1-TDNA-1_A23MHKVLT4_1_vs_1029_2PG-N1-BDNA-1_A23KFG7LT4_1","tumor_sample":"1029_2PG-T1-TDNA-1_A23MHKVLT4_1","normal_sample":"1029_2PG-N1-BDNA-1_A23KFG7LT4_1"},{"pair_id":"1029_38M-T1-TDNA-1_B23MMVMLT4_1_vs_1029_38M-N1-BDNA-1_B23MHTGLT4_1","tumor_sample":"1029_38M-T1-TDNA-1_B23MMVMLT4_1","normal_sample":"1029_38M-N1-BDNA-1_B23MHTGLT4_1"},{"pair_id":"1029_3OA-T1-TDNA-1_A23MHKVLT4_1_vs_1029_3OA-N1-BDNA-1_A23KFG7LT4_1","tumor_sample":"1029_3OA-T1-TDNA-1_A23MHKVLT4_1","normal_sample":"1029_3OA-N1-BDNA-1_A23KFG7LT4_1"},{"pair_id":"1029_3PB-T1-TDNA-1_B23NYJ5LT4_1_vs_1029_3PB-N1-BDNA-1_B23H2GYLT3_1","tumor_sample":"1029_3PB-T1-TDNA-1_B23NYJ5LT4_1","normal_sample":"1029_3PB-N1-BDNA-1_B23H2GYLT3_1"},{"pair_id":"1029_3TP-T1-TDNA-1_A23L3H3LT4_1_vs_1029_3TP-N1-BDNA-1_B23L5TMLT4_1","tumor_sample":"1029_3TP-T1-TDNA-1_A23L3H3LT4_1","normal_sample":"1029_3TP-N1-BDNA-1_B23L5TMLT4_1"},{"pair_id":"1029_3YY-T1-TDNA-1_A23TNLVLT4_1_vs_1029_3YY-N1-BDNA-1_A23MHW3LT4_1","tumor_sample":"1029_3YY-T1-TDNA-1_A23TNLVLT4_1","normal_sample":"1029_3YY-N1-BDNA-1_A23MHW3LT4_1"},{"pair_id":"1029_3YY-T1-TDNA-1_B23MHVMLT4_1_vs_1029_3YY-N1-BDNA-1_A23MHW3LT4_1","tumor_sample":"1029_3YY-T1-TDNA-1_B23MHVMLT4_1","normal_sample":"1029_3YY-N1-BDNA-1_A23MHW3LT4_1"},{"pair_id":"1029_3YY-T1-TDNA-1_B23NN7CLT4_1_vs_1029_3YY-N1-BDNA-1_A23MHW3LT4_1","tumor_sample":"1029_3YY-T1-TDNA-1_B23NN7CLT4_1","normal_sample":"1029_3YY-N1-BDNA-1_A23MHW3LT4_1"},{"pair_id":"1029_4EU-T1-TDNA-1_A23MHKVLT4_1_vs_1029_4EU-N1-BDNA-1_A23KFG7LT4_1","tumor_sample":"1029_4EU-T1-TDNA-1_A23MHKVLT4_1","normal_sample":"1029_4EU-N1-BDNA-1_A23KFG7LT4_1"},{"pair_id":"1029_4FN-T1-TDNA-1_A23MHVGLT4_1_vs_1029_4FN-N1-BDNA-1_B23L5TMLT4_1","tumor_sample":"1029_4FN-T1-TDNA-1_A23MHVGLT4_1","normal_sample":"1029_4FN-N1-BDNA-1_B23L5TMLT4_1"},{"pair_id":"1029_4X0-T1-TDNA-1_B23NYJ5LT4_1_vs_1029_4X0-N1-BDNA-1_B23H2GYLT3_1","tumor_sample":"1029_4X0-T1-TDNA-1_B23NYJ5LT4_1","normal_sample":"1029_4X0-N1-BDNA-1_B23H2GYLT3_1"},{"pair_id":"1029_500-T1-TDNA-1_B23MMVMLT4_1_vs_1029_500-N1-BDNA-1_B23MHTGLT4_1","tumor_sample":"1029_500-T1-TDNA-1_B23MMVMLT4_1","normal_sample":"1029_500-N1-BDNA-1_B23MHTGLT4_1"},{"pair_id":"1029_5CB-T1-TDNA-1_A23MHKVLT4_1_vs_1029_5CB-N1-BDNA-1_A23KFG7LT4_1","tumor_sample":"1029_5CB-T1-TDNA-1_A23MHKVLT4_1","normal_sample":"1029_5CB-N1-BDNA-1_A23KFG7LT4_1"},{"pair_id":"1029_5FF-T1-TDNA-1_B23MHVMLT4_1_vs_1029_5FF-N1-BDNA-1_A23MHW3LT4_1","tumor_sample":"1029_5FF-T1-TDNA-1_B23MHVMLT4_1","normal_sample":"1029_5FF-N1-BDNA-1_A23MHW3LT4_1"},{"pair_id":"1029_5IX-T1-TDNA-1_23FC2GLT4_s14_vs_1029_5IX-N1-BDNA-1_2375WFLT3_s14","tumor_sample":"1029_5IX-T1-TDNA-1_23FC2GLT4_s14","normal_sample":"1029_5IX-N1-BDNA-1_2375WFLT3_s14"},{"pair_id":"1029_5IX-T1-TDNA-1_23K7YCLT4_1_vs_1029_5IX-N1-BDNA-1_235YY7LT3_1","tumor_sample":"1029_5IX-T1-TDNA-1_23K7YCLT4_1","normal_sample":"1029_5IX-N1-BDNA-1_235YY7LT3_1"},{"pair_id":"1029_5KP-T1-TDNA-1_A23MHKVLT4_1_vs_1029_5KP-N1-BDNA-1_A23KFG7LT4_1","tumor_sample":"1029_5KP-T1-TDNA-1_A23MHKVLT4_1","normal_sample":"1029_5KP-N1-BDNA-1_A23KFG7LT4_1"},{"pair_id":"1029_5OV-T1-TDNA-1_A23MHLYLT4_1_vs_1029_5OV-N1-BDNA-1_A23MHW3LT4_1","tumor_sample":"1029_5OV-T1-TDNA-1_A23MHLYLT4_1","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EOF

    aggregate_qc_metrics.py \
        --manifest manifest.json \
        --files-dir . \
        --output variant_qc.json

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC":
    python: $(python --version | sed 's/Python //g')
    aggregate_qc_metrics: 2.0.0
END_VERSIONS