Add cwl and docker files

[lightning.git] / cwl / gvcf2fasta / concat-get_bed_varonlyvcf.cwl

diff --git a/cwl/gvcf2fasta/concat-get_bed_varonlyvcf.cwl b/cwl/gvcf2fasta/concat-get_bed_varonlyvcf.cwl
new file mode 100644 (file)
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+# 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)