multiqc reporting update

cwl/multiqc/multiqc.cwl

@@ -3,45 +3,49 @@
 cwlVersion: v1.0
 class: CommandLineTool
 
-label: "FASTQC run"
+label: "MultiQC reporting"
 
 requirements:
- - class: InlineJavascriptRequirement
- - class: InitialWorkDirRequirement
-   listing:
-    - entry: "$({class: 'Directory', listing: []})"
-      entryname: $(inputs.step)_QualityControl
-      writable: true
-
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entry: "$({class: 'Directory', listing: []})"
+        entryname: "medaka_output"
+        writable: true
+      - entryname: script.sh
+        entry: |-
+          #!/bin/bash
+          source /root/miniconda/bin/activate
+          conda init bash
+          conda activate /unlock/infrastructure/conda/multiqc_v1.12.0
+          multiqc --filename multiqc_report $@
 doc: |
-    Performs quality control on FASTQ file
+    Generates a MultiQC report of a given folder
 
-stdout: fastqc.log
-stderr: fastqc.error
+# stdout: multiqc.log
+# stderr: multiqc.error
 
 inputs:
-  step:
-    type: int
-    doc: workflow step number
-    label: The step number in the workflow
-  fastqs:
-      type: File[]
-      doc: FastQ file directory
-      label: FASTQ file directory
+  folder:
+      type: string
+      doc: Directory path to be processed by MultiQC
+      label: MultiQC directory
       inputBinding:
         position: 100
 
-arguments: ["/unlock/infrastructure/binaries/fastqc_v0.11.9/fastqc", "--outdir", $(inputs.step)_QualityControl]
+baseCommand: ["bash", "script.sh"]
+
+# arguments: ["multiqc","--filename","multiqc_report"]
 
 outputs:
-  info:
-    type: stdout
-  error: 
-    type: stderr
-  upload: 
-    type: Directory
+  # info:
+  #   type: stdout
+  # error: 
+  #   type: stderr
+  multiqc: 
+    type: File
     outputBinding:
-      glob: $(inputs.step)_QualityControl
+      glob: multiqc_report.*
 
 s:author:
   - class: s:Person
@@ -55,7 +59,7 @@ s:author:
 
 s:citation: https://m-unlock.nl
 s:codeRepository: https://gitlab.com/m-unlock/cwl
-s:dateCreated: "2020-00-00"
+s:dateCreated: "2022-00-00"
 s:license: https://spdx.org/licenses/Apache-2.0 
 s:copyrightHolder: "UNLOCK - Unlocking Microbial Potential"