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Adding metatdata and labels
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
generate-report.cwl
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.sample
txt.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