add cwl metadata

runs/fastqc/run.cwl

@@ -16,9 +16,9 @@ steps:
     in:
       fastq: fastq
       finaloutdir: finaloutdir
-    out: [outdir]
+    out: [fastqc_outdir]
 
 outputs:
-  outdir:
+  fastqc_outdir:
     type: Directory
-    outputSource: fastqc/outdir
+    outputSource: fastqc/fastqc_outdir
\ No newline at end of file

workflows/fastqc/fastqc.cwl

@@ -2,12 +2,14 @@
 cwlVersion: v1.2
 class: CommandLineTool
 
-label: Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
+label: FastQC - A high throughput sequence QC analysis tool
 
 doc: |
-  simplified from: https://github.com/common-workflow-library/bio-cwl-tools/blob/66f620da5b0a11e934a6da83272205a2516bcd91/fastqc/fastqc_1.cwl
-  
+  Original docs: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+
   Run fastqc on raw reads in FASTQ format (single or paired end) or aligned reads in BAM.
+  
+  This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/blob/66f620da5b0a11e934a6da83272205a2516bcd91/fastqc/fastqc_1.cwl
 
 hints:
   ResourceRequirement:
@@ -18,11 +20,13 @@ hints:
   SoftwareRequirement:
     packages:
       fastqc:
-        specs: [ https://identifiers.org/biotools/fastqc ]
+        specs: 
+          - https://identifiers.org/biotools/fastqc
+          - - https://identifiers.org/rrid/RRID:SCR_014583
         version: [ "0.11.9" ]
 
-
 baseCommand: "fastqc"
+
 arguments: 
   - valueFrom: $(runtime.outdir)
     prefix: "-o"
@@ -46,3 +50,13 @@ outputs:
     outputBinding:
       glob: "*_fastqc.html"
     
+
+$namespaces:
+  edam: https://edamontology.org/
+  s: https://schema.org/
+$schemas:
+  - https://edamontology.org/EDAM_1.18.owl
+
+s:license: https://spdx.org/licenses/GPL-3.0-or-later
+
+

workflows/fastqc/collectFilesInDir.cwl → workflows/fastqc/gather-files.cwl

 cwlVersion: v1.2
 class: ExpressionTool
-label: Collect files in a directory
+label: Gather files
 doc: |
-  Takes Files (e.g. from a workflow step) and yields them in a desired directory.
+  Helper tool to organize workflow outputs
+
+  Takes an array of files (e.g. from a workflow step) and yields them in a destination directory.
+
+  Adapted from: https://github.com/common-workflow-language/cwl-v1.1/blob/a22b7580c6b50e77c0a181ca59d3828dd5c69143/tests/dir7.cwl
 requirements:
   - class: InlineJavascriptRequirement
 inputs:
-  files: File[]
+  inFiles: File[]
   destination: string
 expression: |
   ${
     return {"outDir": {
       "class": "Directory", 
       "basename": inputs.destination,
-      "listing": inputs.files
+      "listing": inputs.inFiles
     } };
   }
 outputs:

workflows/fastqc/workflow.cwl

@@ -18,15 +18,17 @@ steps:
       fastq: fastq
     out: [fastqc_zip, fastqc_html]
   collectFiles:
-    run: ./collectFilesInDir.cwl
+    run: ./gather-files.cwl
     in: 
-      destination: finaloutdir
-      files:
-        source: [fastqc/fastqc_html, fastqc/fastqc_zip]
+      inFiles:
+        source:
+          - fastqc/fastqc_html
+          - fastqc/fastqc_zip
         linkMerge: merge_flattened
+      destination: finaloutdir
     out: [outDir]
   
 outputs:
-  outdir:
+  fastqc_outdir:
     type: Directory
     outputSource: collectFiles/outDir
\ No newline at end of file

workflows/kallisto/gather-dirs.cwl

@@ -2,8 +2,8 @@ cwlVersion: v1.2
 class: ExpressionTool
 label: Gather directories
 doc: |
-  Helper tool to organize 
-
+  Helper tool to organize workflow outputs
+  
   Takes an array of directories (e.g. from a workflow step) and yields them in a destination directory.
 
   Adapted from: https://github.com/common-workflow-language/cwl-v1.1/blob/a22b7580c6b50e77c0a181ca59d3828dd5c69143/tests/dir7.cwl

workflows/kallisto/kallisto-index.cwl

@@ -26,6 +26,8 @@ doc: |
   -m, --min-size=INT          Length of minimizers (default: automatically chosen)
   -e, --ec-max-size=INT       Maximum number of targets in an equivalence class (default: no maximum)
 
+  This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
+
 hints:
   DockerRequirement:
     dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1

workflows/kallisto/kallisto-quant.cwl

@@ -37,6 +37,9 @@ doc: |
       --verbose                 Print out progress information every 1M proccessed reads
 
 
+  This CWL was adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe
+
+
 hints:
   DockerRequirement:
     dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1