Updating labels and hints on cwl

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index f1cfad4cac14af5825c1cd14209e82ed075b1f93..86d1e1051114ca42f41e956aae55c1d3d9d0028c 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -57,18 +57,18 @@ inputs:
 outputs:
   qc-html:
     type: File[]
-    label: FASTQ QC report
+    label: FASTQ QC reports
     format: edam:format_1964 # HTML
     outputSource: fastqc/out-html
   qc-zip:
     type: File[]
-    label: Zip file of FASTQ QC report and associated data
+    label: Zip files of FASTQ QC report and associated data
     outputSource: fastqc/out-zip 
   gvcf:
     type: File
     outputSource: haplotypecaller/gatheredgvcf
     format: edam:format_3016 # GVCF
-    label: GVCF generated from GATK 
+    label: GVCF generated from GATK Haplotype Caller
   report:
     type: File  
     outputSource: generate-report/report

diff --git a/WGS-processing/cwl/helper/fastqc.cwl b/WGS-processing/cwl/helper/fastqc.cwl
index 888ba926e5f008e8eb126242a5ea00ccdc6ff9b4..e91e88e6e5c0af25a76b7d0e002124ecbc3e9d86 100644 (file)
--- a/WGS-processing/cwl/helper/fastqc.cwl
+++ b/WGS-processing/cwl/helper/fastqc.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Quality check on fastq data using FastQC
+label: Quality check on FASTQ
 
 requirements:
   DockerRequirement:
@@ -10,22 +10,51 @@ requirements:
       - $(inputs.fastq1)
       - $(inputs.fastq2)
 
+hints:
+  SoftwareRequirement:
+    packages:
+      FastQC:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_014583" ]
+        version: [ "0.11.9" ]
+
 inputs:
-  fastq1: File
-  fastq2: File
+  fastq1: 
+    type: File
+    format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R1)
+  fastq2: 
+    type: File
+    format: edam:format_1930 # FASTQ
+    label: One of set of pair-end FASTQs (R2)
 
 outputs:
   out-html:
     type: File[]
+    label: FASTQ QC reports
+    format: edam:format_1964 # HTML
     outputBinding:
       glob: "*html"
   out-zip:
     type: File[]
+    label: Zip files of FASTQ QC report and associated data
+    outputSource: fastqc/out-zip
     outputBinding:
       glob: "*fastqc.zip"
 
 baseCommand: perl
+
 arguments:
   - /FastQC/fastqc
   - $(inputs.fastq1.basename)
   - $(inputs.fastq2.basename)
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$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/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
index 41cfd2e3e195575b642b3476fd9739e275049869..33a1feb9cabbbfc04afee918e6cdadae92a1db89 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Applying base quality score recalibration 
+label: Apply base quality score recalibration 
 
 $namespaces:
   arv: "http://arvados.org/cwl#"