From 50ce3092e09421459358fadeaa60187b1dfa90c5 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 24 Jun 2020 19:46:10 +0000
Subject: [PATCH] Updating labels and hints on cwl
 Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com> no issue #

---
 .../cwl/helper/bwamem-gatk-report-wf.cwl      |  6 ++--
 WGS-processing/cwl/helper/fastqc.cwl          | 35 +++++++++++++++++--
 .../helper/gatk-applyBSQR-with-interval.cwl   |  2 +-
 3 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index f1cfad4..86d1e10 100644
--- 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 888ba92..e91e88e 100644
--- 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 41cfd2e..33a1feb 100644
--- 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#"
-- 
2.30.2