Removing files (moved to subdirs) and updating main wf.

[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
deleted file mode 100644 (file)
index 70ad46c..0000000
--- a/cwl/gvcf2fasta/concat-get_bed_varonlyvcf.cwl
+++ /dev/null
@@ -1,52 +0,0 @@
-# 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
-    tmpdirMin: 2000
-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)