Adding metatdata and labels

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 310753c5c458b849d767e027cae696f8e462576a..41ec58cd35fab6638dd47f2bf078e8d3a032c55a 100644 (file)
--- a/WGS-processing/cwl/helper/annotate-vcf.cwl
+++ b/WGS-processing/cwl/helper/annotate-vcf.cwl
@@ -11,14 +11,24 @@ hints:
   ResourceRequirement:
     ramMin: 10000
     coresMin: 4
   ResourceRequirement:
     ramMin: 10000
     coresMin: 4

+  SoftwareRequirement:
+    packages:
+      BCFtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
+        version: [ "1.10.2" ]

 
 stdout: $(inputs.vcf.nameroot).txt
 
 inputs:
   vcf:
     type: File
 
 stdout: $(inputs.vcf.nameroot).txt
 
 inputs:
   vcf:
     type: File

+    format: edam:format_3016 # VCF
+    label: VCF extracted from GVCF
+    secondaryFiles: [.tbi]

   clinvarvcf:
     type: File
   clinvarvcf:
     type: File

+    format: edam:format_3016 # VCF
+    label: Reference VCF for ClinVar

 
 outputs:
   reporttxt: stdout
 
 outputs:
   reporttxt: stdout


@@ -41,3 +51,11 @@ arguments:
   - query
   - prefix: "-f"
     valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"
   - query
   - prefix: "-f"
     valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"

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

diff --git a/WGS-processing/cwl/helper/generate-report.cwl b/WGS-processing/cwl/helper/generate-report.cwl
index 8ece243530d8cbd6f0ebb02c849783c0c6ba7b60..2652233192e1ac1baba00c985046c81b4fba343f 100644 (file)
--- a/WGS-processing/cwl/helper/generate-report.cwl
+++ b/WGS-processing/cwl/helper/generate-report.cwl
@@ -1,5 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
 cwlVersion: v1.1
 class: CommandLineTool

+label: Generate ClinVar Report

 
 requirements:
   DockerRequirement:
 
 requirements:
   DockerRequirement:


@@ -13,16 +14,27 @@ hints:
 inputs:
   reportfunc:
     type: File
 inputs:
   reportfunc:
     type: File

+    label: Function used to create HTML report

   sampletxt:
     type: File
   sampletxt:
     type: File

+    label: Annotated text from VCF
+  sample:
+    type: string
+    label: Sample Name

   headhtml:
     type: File
   headhtml:
     type: File

+    format: edam:format_2331# HTML
+    label: Header for HTML report

   tailhtml:
     type: File
   tailhtml:
     type: File

+    format: edam:format_2331 # HTML
+    label: Footer for HTML report

 
 outputs:
   report:
     type: File
 
 outputs:
   report:
     type: File

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

     outputBinding:
       glob: "*html"
 
     outputBinding:
       glob: "*html"
 


@@ -31,6 +43,14 @@ baseCommand: python
 arguments:
   - $(inputs.reportfunc)
   - $(inputs.sampletxt)
 arguments:
   - $(inputs.reportfunc)
   - $(inputs.sampletxt)

-  - $(inputs.sampletxt.basename)
+  - $(inputs.sample)

   - $(inputs.headhtml)
   - $(inputs.tailhtml)
   - $(inputs.headhtml)
   - $(inputs.tailhtml)

+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$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 6a0f18d8fa0eedf7b0d90cf3defc942e72114317..b53f385d85d690fbe4b7a5d241254f0add9618f4 100644 (file)
--- a/WGS-processing/cwl/helper/report-wf.cwl
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -51,6 +51,7 @@ steps:
     in:
       reportfunc: reportfunc
       sampletxt: annotate/reporttxt
     in:
       reportfunc: reportfunc
       sampletxt: annotate/reporttxt

+      sample: sample

       headhtml: headhtml
       tailhtml: tailhtml
     out: [report]
       headhtml: headhtml
       tailhtml: tailhtml
     out: [report]