.command.sh - Workdir - NFCORE_SAREK:SAREK:GENERATE_CHIP_REPORT (Sig_18_Blood)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/967cbfd53b70457eb364b7015fbf71/.command.sh
Size: 438 bytes
Task: NFCORE_SAREK:SAREK:GENERATE_CHIP_REPORT (Sig_18_Blood)
Attempt

Content

#!/bin/bash -Ceuo pipefail
generate_chip_report.py \
    --vcf Sig_18_Blood.deconflicted_chip.vcf.gz \
    --output Sig_18_Blood.chip_report.vcf.gz

tabix -p vcf Sig_18_Blood.chip_report.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:GENERATE_CHIP_REPORT":
    generate_chip_report: $(generate_chip_report.py --version 2>&1 || echo "1.0.0")
    cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
END_VERSIONS