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

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/3ab5a7a32117c9dbc74856e5b5423f/.command.sh
Size: 407 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_GENEMETRICS (HCC1395_tumor_vs_HCC1395_BL)
Attempt

Content

#!/bin/bash -Ceuo pipefail
cnvkit.py \
    genemetrics \
    HCC1395_tumor.recalibrated.cnr \
    --segment HCC1395_tumor.recalibrated.cns \
    --output HCC1395_tumor.recalibrated.genemetrics.tsv \


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