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 be3483c5b354353b40ee3cf8e726501c879b2249..310753c5c458b849d767e027cae696f8e462576a 100644 (file)
--- 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 dfa3e248da1c19dcd5426cdee894dcd0e8d81f96..305227e9c7e7463f0a58b43be6d2d119b0af835e 100644 (file)
--- 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 0029018394d7aa1c2dd170860196efef9ed39a3a..6a0f18d8fa0eedf7b0d90cf3defc942e72114317 100644 (file)
--- 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: