.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT (HCC1395_tumor_vs_HCC1395_BL)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/aa32b581e1985f130422d83d2d0827/.command.sh
Size: 355 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
cnvkit.py export \
    vcf \
    HCC1395_tumor.recalibrated.somatic.call.cns \
    -o HCC1395_tumor_vs_HCC1395_BL.cnvcall.vcf

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_EXPORT":
    cnvkit: $(cnvkit.py version | sed -e 's/cnvkit v//g')
END_VERSIONS