--- /dev/null
+# Copyright (C) The Lightning Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+cwlVersion: v1.1
+class: CommandLineTool
+label: Concatenate and get no call BED and variant only VCF from gVCF
+requirements:
+ ShellCommandRequirement: {}
+hints:
+ DockerRequirement:
+ dockerPull: vcfutil
+ ResourceRequirement:
+ ramMin: 5000
+ outdirMin: 40000
+inputs:
+ sampleid:
+ type: string
+ label: Sample ID
+ splitvcfdir:
+ type: Directory
+ label: Input directory of split gVCFs
+ gqcutoff:
+ type: int
+ label: GQ (Genotype Quality) cutoff for filtering
+ genomebed:
+ type: File
+ label: Whole genome BED
+ bashscript:
+ type: File
+ label: Script to untar and concatenate vcf tar ball
+ default:
+ class: File
+ location: src/concat-get_bed_varonlyvcf.sh
+outputs:
+ nocallbed:
+ type: File
+ label: No call BED of gVCF
+ outputBinding:
+ glob: "*_nocall.bed"
+ varonlyvcf:
+ type: File
+ label: Variant only VCF
+ outputBinding:
+ glob: "*_varonly.vcf.gz"
+ secondaryFiles: [.tbi]
+arguments:
+ - $(inputs.bashscript)
+ - $(inputs.sampleid)
+ - $(inputs.splitvcfdir)
+ - $(inputs.gqcutoff)
+ - $(inputs.genomebed)