.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/af/55d8a76980f8811038de3f5611b85d/.command.sh
Size: 591 bytes
Task: NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation)
Attempt

Content

#!/bin/bash -Ceuo pipefail
cat << 'EOF' > manifest.json
{"pairs":[{"pair_id":"HCC1395_tumor_vs_HCC1395_BL","tumor_sample":"HCC1395_tumor","normal_sample":"HCC1395_BL"},{"pair_id":"custom_Sig_18_tumor_normal","tumor_sample":"Sig_18_tissue","normal_sample":"Sig_18_Blood"}],"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