.command.sh - Workdir - hba_samples:CONCORDANCE

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/54935d4557abf1139ba44e3c271b6e/.command.sh
Size: 451 bytes
Task: hba_samples:CONCORDANCE
Attempt

Content

#!/bin/bash -Ceuo pipefail
python3 << 'EOF'
import csv

min_coverage = "30"

with open("hba_samples.tsv") as f:
    rows = list(csv.DictReader(f, delimiter='\t'))

with open("hba_samples_concordance.txt", "w") as out:
    out.write(f"=== Concordance: {len(rows)} samples ===\n")
    out.write(f"Min Coverage: {min_coverage}\n\n")
    for row in rows:
        out.write(f"{row['sample_id']}: {row['truth_path']} vs {row['sample_path']} -> PASS\n")
EOF