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Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/6c561bcd6b7ad7cefdeadb8208cec4/.command.sh
Size
2.9 KB
Task
DAQ:CONTROL_METRICS:MERGE_CONTROL_METRICS (merge_control_metrics)
Attempt

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#!/bin/bash -Ceuo pipefail
cat <<'EOF' > manifest.json
[{"control_type":"positive_somatic","sample_id":"Sig_18_tissue","variant_type":"mimsi","file":"positive_somatic_control_2.mimsi.tsv"},{"control_type":"positive_somatic","sample_id":"HCC1395_tumor","variant_type":"mimsi","file":"positive_somatic_control_1.mimsi.tsv"},{"control_type":"negative_somatic","sample_id":"HCC1395_BL","variant_type":"mimsi","file":"negative_somatic_control_1.mimsi.tsv"},{"control_type":"negative_somatic","sample_id":"Sig_18_Blood","variant_type":"msi","file":"negative_somatic_control_2.msi.tsv"},{"control_type":"negative_somatic","sample_id":"HCC1395_BL","variant_type":"msi","file":"negative_somatic_control_1.msi.tsv"},{"control_type":"positive_somatic","sample_id":"Sig_18_tissue","variant_type":"msi","file":"positive_somatic_control_2.msi.tsv"},{"control_type":"negative_somatic","sample_id":"Sig_18_Blood","variant_type":"mimsi","file":"negative_somatic_control_2.mimsi.tsv"},{"control_type":"positive_somatic","sample_id":"HCC1395_tumor","variant_type":"msi","file":"positive_somatic_control_1.msi.tsv"},{"control_type":"germline","sample_id":"HCC1395_BL","variant_type":"snv_indel","file":"germline_control_1.snv_indel.tsv"},{"control_type":"germline","sample_id":"Sig_18_Blood","variant_type":"snv_indel","file":"germline_control_2.snv_indel.tsv"},{"control_type":"positive_somatic","sample_id":"HCC1395_tumor","variant_type":"tmb","file":"positive_somatic_control_1.tmb.tsv"},{"control_type":"negative_somatic","sample_id":"Sig_18_Blood","variant_type":"tmb","file":"negative_somatic_control_2.tmb.tsv"},{"control_type":"negative_somatic","sample_id":"HCC1395_BL","variant_type":"tmb","file":"negative_somatic_control_1.tmb.tsv"},{"control_type":"negative_somatic","sample_id":"HCC1395_BL","variant_type":"snv_indel","file":"negative_somatic_control_1.snv_indel.tsv"},{"control_type":"negative_somatic","sample_id":"Sig_18_Blood","variant_type":"snv_indel","file":"negative_somatic_control_2.snv_indel.tsv"},{"control_type":"positive_somatic","sample_id":"HCC1395_tumor","variant_type":"snv_indel","file":"positive_somatic_control_1.snv_indel.tsv"},{"control_type":"positive_somatic","sample_id":"Sig_18_tissue","variant_type":"tmb","file":"positive_somatic_control_2.tmb.tsv"},{"control_type":"positive_somatic","sample_id":"Sig_18_tissue","variant_type":"snv_indel","file":"positive_somatic_control_2.snv_indel.tsv"},{"control_type":"germline","sample_id":"HCC1395_BL","variant_type":"cnv","file":"germline_control_1.cnv.tsv"},{"control_type":"germline","sample_id":"Sig_18_Blood","variant_type":"cnv","file":"germline_control_2.cnv.tsv"}]
EOF

merge_control_metrics.py \
    --manifest manifest.json \
    --files-dir data \
    --output-csv  control_metrics.csv \
    --output-json control_metrics.json

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_METRICS:MERGE_CONTROL_METRICS":
    python: $(python --version | sed 's/Python //g')
    merge_control_metrics: 1.1.0
END_VERSIONS