Removing white spaces and commenting schemas

[arvados-tutorial.git] / WGS-processing / cwl / helper / fastqc.cwl

diff --git a/WGS-processing/cwl/helper/fastqc.cwl b/WGS-processing/cwl/helper/fastqc.cwl
index 888ba926e5f008e8eb126242a5ea00ccdc6ff9b4..30193a12a3a27225ee56ff28dc071e5184fc57d6 100644 (file)
--- a/WGS-processing/cwl/helper/fastqc.cwl
+++ b/WGS-processing/cwl/helper/fastqc.cwl
@@ -1,31 +1,54 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Quality check on fastq data using FastQC
+label: Quality check on FASTQ
 
 requirements:
   DockerRequirement:
-    dockerPull: curii/fastqc
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.fastq1)
-      - $(inputs.fastq2)
+    dockerPull: biocontainers/fastqc:v0.11.9_cv6
+
+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
     outputBinding:
       glob: "*fastqc.zip"
 
-baseCommand: perl
+baseCommand: fastqc
+
 arguments:
-  - /FastQC/fastqc
-  - $(inputs.fastq1.basename)
-  - $(inputs.fastq2.basename)
+  - $(inputs.fastq1.path)
+  - $(inputs.fastq2.path)
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl