.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL (custom_Sig_18_tumor_normal)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/9f31c1fa91229a2f0b1c8af38b7a85/.command.sh
Size: 346 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL (custom_Sig_18_tumor_normal)
Attempt

Content

#!/bin/bash -Ceuo pipefail
cnvkit.py call \
    Sig_18_tissue.recalibrated.cns \
     \
     \
    -o Sig_18_tissue.recalibrated.somatic.call.cns

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