From 7bf5762dade2f8b6d87a848973e5cfd02f47ab55 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 1 Jul 2020 16:00:28 +0000
Subject: [PATCH] Adding metadata and step renaming
 Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com> no issue #

---
 WGS-processing/cwl/helper/gather-vcf.cwl      | 26 ++++++++++++++++---
 .../helper/scatter-gatk-wf-with-interval.cwl  |  6 ++---
 2 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/WGS-processing/cwl/helper/gather-vcf.cwl b/WGS-processing/cwl/helper/gather-vcf.cwl
index cd1532c..15b6551 100644
--- a/WGS-processing/cwl/helper/gather-vcf.cwl
+++ b/WGS-processing/cwl/helper/gather-vcf.cwl
@@ -1,6 +1,7 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Gathering vcf using Picard 
+label: Gather GVCF using Picard 
+
 $namespaces:
   arv: "http://arvados.org/cwl#"
   cwltool: "http://commonwl.org/cwltool#"
@@ -21,11 +22,15 @@ hints:
 inputs:
   gvcfdir: 
     type: Directory
-    label: Input directory of gvcfs
+    label: Input directory of GVCFs
     loadListing: 'shallow_listing'
-  sample: string
+  sample: 
+    type: string
+    label: Sample Name
   reference:
     type: File
+    format: edam:format_1929 # FASTA
+    label: Reference genome
     secondaryFiles:
       - .amb
       - .ann
@@ -37,6 +42,8 @@ inputs:
 outputs:
   gatheredgvcf:
     type: File
+    format: edam:format_3016 # GVCF
+    label: Gathered GVCF 
     secondaryFiles:
       - .tbi
     outputBinding:
@@ -82,3 +89,16 @@ arguments:
       }
   - prefix: "-O"
     valueFrom: $(inputs.sample).g.vcf.gz
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl
diff --git a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
index 17bb13e..45653db 100644
--- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@ -42,10 +42,10 @@ outputs:
   gatheredgvcf:
     type: File
     format: edam:format_3016 # GVCF
-    label: GVCF generated from GATK Haplotype Caller
+    label: Gathered GVCF 
     secondaryFiles: 
       - .tbi
-    outputSource: merge-GVCFs/gatheredgvcf
+    outputSource: gather-GVCFs/gatheredgvcf
     
 steps:
   splitintervals:
@@ -67,7 +67,7 @@ steps:
       intervallist: splitintervals/intervalfiles
     out: [gvcf]
 
-  merge-GVCFs:
+  gather-GVCFs:
     run: gather-array-vcf.cwl
     in:
       gvcfarray: recal-haplotypecaller/gvcf
-- 
2.30.2