new combined and more complete table of bins

cwl/metagenomics/bin_assembly_stats.cwl

@@ -10,35 +10,60 @@ doc: |
     + table of the bins and their respective assembly contigs names.
 
 requirements:
- - class: InlineJavascriptRequirement 
+  - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+    - entry: "$({class: 'Directory', listing: []})"
+      entryname: "Bins summary table"
+      writable: true
+    - entryname: script.sh
+      entry: |-
+        #!/bin/bash
+        source /unlock/infrastructure/venv/bin/activate
+        python3 /unlock/infrastructure/binaries/scripts/metagenomics/bins_summary.py $@
+
+
+baseCommand: ["bash", "script.sh"] # see requirements
 
 inputs:
   identifier:
     type: string
     doc: Identifier for this dataset used in this workflow
-    label: identifier used
-  
+    label: identifier used  
   bin_dir:
     type: Directory
-    doc: folder containing bins in fasta format from metagenomic binning
-    label: bins folder
+    doc: Directory containing bins in fasta format from metagenomic binning
+    label: Bins directory
+    inputBinding:
+      prefix: "--bin_dir"
+  bin_depths:
+    type: File
+    doc: MetaBAT2 aggregateDepths file
+    label: bin depths
+    inputBinding:
+      prefix: "--bin_depths"
+  busco_dir:
+    type: Directory 
+    doc: Directory containing BUSCO reports
+    label: BUSCO folder
+    inputBinding:
+      prefix: "--busco_dir"
+  checkm:
+    type: File
+    doc: CheckM report file
+    label: CheckM report
+    inputBinding:
+      prefix: "--checkm"
 
 arguments:
-  - "$(inputs.bin_dir)"
-
-baseCommand: [bash, "/unlock/infrastructure/binaries/scripts/metagenomics/bin_assembly_stats.sh"]
-
-stdout: $(inputs.identifier)_binAssemblyStats.tsv
+  - prefix: "--output_file"
+    valueFrom: $(inputs.identifier)_bin_summary.tsv
 
 outputs:
-  binStats:
-    type: File
-    outputBinding:
-      glob: $(inputs.identifier)_binAssemblyStats.tsv
-  binContigs:
+  bin_summary:
     type: File
     outputBinding:
-      glob: binContigs.tsv
+      glob: $(inputs.identifier)_bin_summary.tsv
 
 s:author:
   - class: s:Person