#!/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