Adding labels and formats to cwl

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 019fa1ab5d53f65982928ec7a74197e76340a321..be3483c5b354353b40ee3cf8e726501c879b2249 100644 (file)
--- a/WGS-processing/cwl/helper/annotate-vcf.cwl
+++ b/WGS-processing/cwl/helper/annotate-vcf.cwl
@@ -1,5 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
 cwlVersion: v1.1
 class: CommandLineTool

+label: Annotating and Filtering VCF

 
 requirements:
   - class: DockerRequirement
 
 requirements:
   - class: DockerRequirement

diff --git a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
index f53516b8ebb8beeb16e51f4f7b1e251d424077cb..c539325544572fc3968cb979fe4617723f26601a 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
+++ b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
@@ -1,6 +1,7 @@
 cwlVersion: v1.1
 class: CommandLineTool
 cwlVersion: v1.1
 class: CommandLineTool

-label: Realigning fastqs and converting output to bam
+label: Aligning fastqs with BWA
+

 $namespaces:
   arv: "http://arvados.org/cwl#"
   cwltool: "http://commonwl.org/cwltool#"
 $namespaces:
   arv: "http://arvados.org/cwl#"
   cwltool: "http://commonwl.org/cwltool#"

diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index 89237b1ad894825235228da8ea1016ec1670c3b0..a6218bdaa79bd28f83a2cd91087fca673999cf8a 100644 (file)
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -1,15 +1,19 @@
 cwlVersion: v1.1
 class: Workflow
 cwlVersion: v1.1
 class: Workflow

-label: Main WGS Processing Workflow
+label: WGS processing workflow scattered over samples

 
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: ScatterFeatureRequirement
 
 inputs:
 
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: ScatterFeatureRequirement
 
 inputs:

-  fastqdir: Directory 
+  fastqdir:
+    type: Directory 
+    label: Directory of paired FASTQ files

   reference:
     type: File
   reference:
     type: File

+    format: edam:format_1929 # FASTA
+    label: Reference genome 

     secondaryFiles:
       - .amb
       - .ann
     secondaryFiles:
       - .amb
       - .ann


@@ -18,24 +22,46 @@ inputs:
       - .sa
       - .fai
       - ^.dict
       - .sa
       - .fai
       - ^.dict

-  sample: string
+  sample: 
+    type: string
+    label: Sample name

   knownsites:
     type: File
   knownsites:
     type: File

+    format: edam:format_3016 # VCF
+    label: VCF of known polymorphic sites for BQSR

     secondaryFiles:
       - .tbi   
     secondaryFiles:
       - .tbi   

-  scattercount: string
-  clinvarvcf: File
-  reportfunc: File
-  headhtml: File
-  tailhtml: File
+  scattercount: 
+    type: string
+    label: Desired split for variant calling
+  clinvarvcf: 
+    type: File
+    format: edam:format_3016 # VCF
+    label: Reference VCF for ClinVar
+  reportfunc: 
+    type: File
+    label: Function used to create HTML report
+  headhtml: 
+    type: File
+    format: edam:format_1964 # HTML
+    label: Header for HTML report
+  tailhtml: 
+    type: File
+    format: edam:format_1964 # HTML
+    label: Footer for HTML report

 
 outputs:
   gvcf:
     type: File[]
     outputSource: bwamem-gatk-report/gvcf
 
 outputs:
   gvcf:
     type: File[]
     outputSource: bwamem-gatk-report/gvcf

+    format: edam:format_3016 # GVCF
+    label: GVCFs generated from sets of fastqs
+    

   report:
     type: File[]  
     outputSource: bwamem-gatk-report/report
   report:
     type: File[]  
     outputSource: bwamem-gatk-report/report

+    format: edam:format_1964 # HTML
+    label: ClinVar variant reports 

 
 steps:
   getfastq:
 
 steps:
   getfastq:


@@ -65,4 +91,9 @@ s:codeRepository: https://github.com/arvados/arvados-tutorial
 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
 
 $namespaces:
 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
 
 $namespaces:

-  s: https://schema.org/
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl