From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 1 Jul 2020 17:47:34 +0000 (+0000)
Subject: Adding metadata, updating variables
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/a5a391be09c8e08c5b35ac0ba76f5d9634e6ed41

Adding metadata, updating variables
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

diff --git a/WGS-processing/cwl/helper/annotate-vcf.cwl b/WGS-processing/cwl/helper/annotate-vcf.cwl
index be3483c..310753c 100644
--- a/WGS-processing/cwl/helper/annotate-vcf.cwl
+++ b/WGS-processing/cwl/helper/annotate-vcf.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Annotating and Filtering VCF
+label: Annotate and filter VCF
 
 requirements:
   - class: DockerRequirement
@@ -19,6 +19,7 @@ inputs:
     type: File
   clinvarvcf:
     type: File
+
 outputs:
   reporttxt: stdout
 
diff --git a/WGS-processing/cwl/helper/gvcf-to-vcf.cwl b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
index dfa3e24..305227e 100644
--- a/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
+++ b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Converts gvcf to vcf
+label: Convert GVCF to VCF 
 
 requirements:
   - class: DockerRequirement
@@ -11,16 +11,28 @@ hints:
   ResourceRequirement:
     ramMin: 10000
     coresMin: 4
-
+  SoftwareRequirement:
+    packages:
+      BCFtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
+        version: [ "1.10.2" ]
+      HTSlib:
+        version: [ "1.10.2" ]
+        
 inputs:
-  samplename:
+  sample:
     type: string
+    label: Sample Name
   gvcf:
     type: File
+    format: edam:format_3016 # GVCF
+    label: GVCF generated from GATK
   
 outputs:
   vcf:
     type: File
+    format: edam:format_3016 # VCF
+    label: VCF extracted from GVCF
     outputBinding:
       glob: "*.vcf.gz"
     secondaryFiles: [.tbi]
@@ -35,10 +47,21 @@ arguments:
     valueFrom: "AVG(GQ)>20"
   - valueFrom: "-Ov"
   - prefix: "-o"
-    valueFrom: $(inputs.samplename).vcf
+    valueFrom: $(inputs.sample).vcf
   - {valueFrom: '&&', shellQuote: false}
   - bgzip
-  - valueFrom: $(inputs.samplename).vcf
+  - valueFrom: $(inputs.sample).vcf
   - {valueFrom: '&&', shellQuote: false}
   - tabix
-  - valueFrom: $(inputs.samplename).vcf.gz
+  - valueFrom: $(inputs.sample).vcf.gz
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl
diff --git a/WGS-processing/cwl/helper/report-wf.cwl b/WGS-processing/cwl/helper/report-wf.cwl
index 0029018..6a0f18d 100644
--- a/WGS-processing/cwl/helper/report-wf.cwl
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -7,7 +7,7 @@ inputs:
     type: File
     format: edam:format_3016 # GVCF
     label: Gathered GVCF
-  samplename:
+  sample:
     type: string
     label: Sample Name
   clinvarvcf:
@@ -38,16 +38,14 @@ steps:
     run: gvcf-to-vcf.cwl
     in:
       gvcf: gvcf
-      samplename: samplename
+      sample: sample
     out: [vcf]
-
   annotate:
     run: annotate-vcf.cwl
     in:
       vcf: gvcf-to-vcf/vcf
       clinvarvcf: clinvarvcf
     out: [reporttxt]
-
   generate-report:
     run: generate-report.cwl
     in: