From 22f7e3b6540d16b1c7cfff1735e1553f7241c540 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 1 Jul 2020 18:42:15 +0000
Subject: [PATCH] Adding metatdata and labels Arvados-DCO-1.1-Signed-off-by:
 Sarah Wait Zaranek <swz@curii.com> no issue #

---
 WGS-processing/cwl/helper/annotate-vcf.cwl    | 18 +++++++++++++++
 WGS-processing/cwl/helper/generate-report.cwl | 22 ++++++++++++++++++-
 WGS-processing/cwl/helper/report-wf.cwl       |  1 +
 3 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/WGS-processing/cwl/helper/annotate-vcf.cwl b/WGS-processing/cwl/helper/annotate-vcf.cwl
index 310753c..41ec58c 100644
--- 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
+  SoftwareRequirement:
+    packages:
+      BCFtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
+        version: [ "1.10.2" ]
 
 stdout: $(inputs.vcf.nameroot).txt
 
 inputs:
   vcf:
     type: File
+    format: edam:format_3016 # VCF
+    label: VCF extracted from GVCF
+    secondaryFiles: [.tbi]
   clinvarvcf:
     type: File
+    format: edam:format_3016 # VCF
+    label: Reference VCF for ClinVar
 
 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"
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$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 8ece243..2652233 100644
--- 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
+label: Generate ClinVar Report
 
 requirements:
   DockerRequirement:
@@ -13,16 +14,27 @@ hints:
 inputs:
   reportfunc:
     type: File
+    label: Function used to create HTML report
   sampletxt:
     type: File
+    label: Annotated text from VCF
+  sample:
+    type: string
+    label: Sample Name
   headhtml:
     type: File
+    format: edam:format_2331# HTML
+    label: Header for HTML report
   tailhtml:
     type: File
+    format: edam:format_2331 # HTML
+    label: Footer for HTML report
 
 outputs:
   report:
     type: File
+    format: edam:format_1964 # HTML
+    label: ClinVar variant report
     outputBinding:
       glob: "*html"
 
@@ -31,6 +43,14 @@ baseCommand: python
 arguments:
   - $(inputs.reportfunc)
   - $(inputs.sampletxt)
-  - $(inputs.sampletxt.basename)
+  - $(inputs.sample)
   - $(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 6a0f18d..b53f385 100644
--- 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
+      sample: sample
       headhtml: headhtml
       tailhtml: tailhtml
     out: [report]
-- 
2.30.2