.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/97/2c9ca252d52205d48f791f07c2602a/.command.sh
Size: 562 bytes
Task: NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC (variant_qc_aggregation)
Attempt

Content

#!/bin/bash -Ceuo pipefail
cat << 'EOF' > manifest.json
{"pairs":[{"pair_id":"659_csY-T1-TDNA-1_A23FG3YLT4_1_vs_659_csY-N1-BDNA-1_A23FG3YLT4_1","tumor_sample":"659_csY-T1-TDNA-1_A23FG3YLT4_1","normal_sample":"659_csY-N1-BDNA-1_A23FG3YLT4_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