.command.sh - Workdir - NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/87279f4c85db0bb7ba8ff7dbe50ea4/.command.sh
Size: 6.2 KB
Task: NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation)
Attempt
Content

#!/bin/bash -Ceuo pipefail
cat << 'EOF' > manifest.json
{"pairs":[{"pair_id":"pos_somatic_000","tumor_sample":"FFPE_HD789_01_gDNA_0001_A23KYMYLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_001","tumor_sample":"FFPE_HD789_01_gDNA_0001_A23L5NJLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_002","tumor_sample":"FFPE_HD789_01_gDNA_0001_23FC2GLT4_s47","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_003","tumor_sample":"FFPE_HD789_01_gDNA_0001_23K7YCLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_004","tumor_sample":"FFPE_HD789_01_p1_gDNA_0001_A23L3H3LT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_005","tumor_sample":"FFPE_HD789_01_p1_gDNA_0001_A23MHLYLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_006","tumor_sample":"FFPE_HD789_01_p1_gDNA_0001_B23MHVMLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_007","tumor_sample":"FFPE_HD789_01_p1_gDNA_0001_B23MMVMLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_008","tumor_sample":"FFPE_HD789_01_p1_gDNA_0002_A23MHVGLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_009","tumor_sample":"FFPE_HD789_01_p1_gDNA_0002_B23KCGWLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_010","tumor_sample":"FFPE_HD789_01_p1_gDNA_0002_B23MHWGLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_011","tumor_sample":"FFPE_HD789_01_p1_gDNA_0003_A23KCGYLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_012","tumor_sample":"FFPE_HD789_01_p1_gDNA_0003_A23MCTVLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_013","tumor_sample":"FFPE_HD789_01_p1_gDNA_0003_A23MHTWLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_014","tumor_sample":"FFPE_HD789_01_p1_gDNA_0004_A23MHTWLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_015","tumor_sample":"FFPE_HD789_01_p1_gDNA_0004_B23KFCWLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_016","tumor_sample":"FFPE_HD789_01_p1_gDNA_0004_B23MCVGLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_017","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_A23FG3YLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_018","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_A23H5VJLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_019","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_A23LGTTLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_020","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_A23MHKLLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_021","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_A23MJ3TLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_022","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_A23NYHCLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_023","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_B23KKT2LT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_024","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_B23LG35LT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_025","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_B23LG3FLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_026","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_B23MHJYLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_027","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_B23NLHKLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_028","tumor_sample":"FFPE_HD789_01_p1_gDNA_0005_B23NYJ5LT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_029","tumor_sample":"FFPE_HD789_01_p2_gDNA_01_A23KC75LT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_030","tumor_sample":"FFPE_HD789_01_p2_gDNA_01_A23MHKVLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_031","tumor_sample":"FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_032","tumor_sample":"FFPE_HD789_01_p2_gDNA_01_B23KCHGLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_033","tumor_sample":"FFPE_HD789_01_p2_gDNA_01_B23MHVHLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_034","tumor_sample":"FFPE_HD789_01_p2_gDNA_01_B23MHVNLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_035","tumor_sample":"FFPE_HD789_01_p2_gDNA_02_A23KFCVLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_036","tumor_sample":"FFPE_HD789_01_p2_gDNA_02_B23KCK5LT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_037","tumor_sample":"FFPE_HD789_01_p2_gDNA_02_B23MF2NLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_038","tumor_sample":"FFPE_HD789_01_p2_gDNA_03_A23GW7HLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_039","tumor_sample":"FFPE_HD789_01_p2_gDNA_03_A23MYM7LT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_040","tumor_sample":"FFPE_HD789_01_p2_gDNA_03_A23NLJYLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"},{"pair_id":"pos_somatic_041","tumor_sample":"FFPE_HD789_01_p2_gDNA_03_B23NYHYLT4_1","normal_sample":"NA12878_c_0002_gDNA_0005_B23KYWJLT4_1"}],"qc_files":[]}
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