random edits, don't merge

CWL/Tools/bowtie2.tool.cwl

@@ -24,9 +24,8 @@ requirements:
          var re = new RegExp("^" + inputs.index , "i");
          var files = inputs.indexDir.listing ;
          for (var f in files) {
-            var file = files[f] ;
+           var file = files[f] ;
            if ( re.test(file.basename) ){ list.push(file) }
-           else { list.push(inputs.index)}
          }
 
          return list;
@@ -85,7 +84,7 @@ outputs:
     type: stderr  
 
 
-$namespaces:
-  Formats: FileFormats.cv.yaml
+# $namespaces:
+#  Formats: FileFormats.cv.yaml
 # s:license: "https://www.apache.org/licenses/LICENSE-2.0"
-# s:copyrightHolder: "MG-RAST"
+# s:copyrightHolder: "MG-RAST"

CWL/Tools/cutadapt.tool.cwl

@@ -29,50 +29,44 @@ stderr: cutadapt.error
 #            -o db/SILVA.${prok_forward}.${prok_reverse}
 
 inputs:
-  g:
+  five_prime_adapter:
     label: prok_forward
     doc: 5’ adapter 
     type: string
     inputBinding:
       prefix: -g
-  a:
+  three_prime_adapter:
     label: prok_reverse
     doc: 3’ adapter  
     type: string                        
     inputBinding:
       prefix: -a
   format:
-    label: format
-    doc:  <fasta|fastq|sra-fastq>
+    doc:  <fasta|fastq|sra-fastq>  # candidate for becoming an enum
     type: string                        
     inputBinding:
       prefix: -f    
   error:
-    label: error_rate
-    doc:  Maximum allowed error rate  
-    type: string                        
+    label:  Maximum allowed error rate  
+    type: string  # really?
     inputBinding:
       prefix: -e    
   discard-untrimmed:
-    label: discard-untrimmed
     doc: Discard reads that do not contain the adapter
     type: boolean?                        
     inputBinding:
       prefix: --discard-untrimmed
   trimmed-only:
-    label: trimmed-only
-    doc: .
+    doc: FIXME
     type: boolean?
     inputBinding:
       prefix: --trimmed-only          
   output:
-    label: output
     doc:  Write reads to OUTPUT
     type: string
     inputBinding:
       prefix: -o
   sequences:
-    label: 
     doc: input sequences
     type: File
     inputBinding:

CWL/Workflows/create_primer.workflow.cwl

@@ -5,25 +5,23 @@ label: Create ePCR version for primers
 doc: prepare UNITE and SIVLA fasta database files and taxonomy tables using cutadapt 
 
 requirements:
-  - class: StepInputExpressionRequirement
-  - class: InlineJavascriptRequirement
-  - class: ScatterFeatureRequirement
-  - class: MultipleInputFeatureRequirement
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  ScatterFeatureRequirement: {}
+  MultipleInputFeatureRequirement: {}
 
 inputs:
   euka_sequences:
-    # /usr/local/share/db/UNITE*.fasta
+    # /usr/local/share/db/UNITE*.fasta   # MRC: One, or many files?
     type: File
-    format:
-      - fasta
+    format: edam:format_1929  # FASTA
   euka_forward: string
   euka_reverse: string
   prok_sequences:
-    # /usr/local/share/db/SILVA*.fasta 
+    # /usr/local/share/db/SILVA*.fasta   # MRC: One, or many files?
     type: File
-    format:
-      - fasta
-  prok_forward: string
+    format: edam:format_1929  # FASTA
+  prok_forward: string   # Is this barcode?
   prok_reverse: string
   error:
     type: string?
@@ -34,9 +32,11 @@ outputs:
   classified_euk:
     type: File
     outputSource: euk/processed
+    # format: # ???
   classified_prok:
     type: File
     outputSource: prok/processed  
+    # format: # ???
 
 
 
@@ -84,3 +84,13 @@ steps:
        source: [prok_sequences , prok_forward , prok_reverse]
        valueFrom: $(self[0].basename).$(self[1]).$(self[2])
     out: [processed]
+
+$namespaces:
+  - edam: http://edamontology.org/
+  - s: http://schema.org/
+$schemas:
+ - http://edamontology.org/EDAM_1.18.owl
+ - https://schema.org/docs/schema_org_rdfa.html
+
+# s:license: "https://www.apache.org/licenses/LICENSE-2.0"
+# s:copyrightHolder: "FIXME"

CWL/Workflows/decompress_mate_pair.workflow.cwl

@@ -5,21 +5,17 @@ label: Decompress
 doc: Decompress mate pair fastq files
 
 requirements:
-  - class: StepInputExpressionRequirement
-  - class: InlineJavascriptRequirement
-  - class: ScatterFeatureRequirement
-  - class: MultipleInputFeatureRequirement
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  ScatterFeatureRequirement: {}
+  MultipleInputFeatureRequirement: {}
+  SchemaDefRequirement:
+    types:
+      - $import: ../mate_pair.yml
+
 
 inputs:
-  mate_pair:
-      type:
-        type: record
-        label: mate_pair
-        fields:
-          forward:
-            type: File
-          reverse:
-            type: File
+  mate_pair: mate_pair
   stage:
     type: string
     default: "0010"        
@@ -32,7 +28,7 @@ outputs:
     outputSource: [decompress_forward/decompressed , decompress_reverse/decompressed]
   mate_pair_decompressed: 
     outputSource: make_return/mate_pair
-    type: Any 
+    type: ../mate_pair.yml#mate_pair
 
 
 steps:
@@ -96,7 +92,7 @@ steps:
           type: File
       outputs:
         mate_pair:
-          type: Any
+          type: ../mate_paire.yml#mate_pair
       expression: |
                 ${
                   var mate_pair = {

CWL/Workflows/primer.job.cwl

@@ -2,7 +2,7 @@ sequences:
   class: File
   path: ../Data/Inputs/sequences.all.fasta
   # /usr/local/share/db/UNITE*.fasta
-  format: fasta
+  format: edam:format_1929  # FASTA
 
 primer: 
   eukaryote:
@@ -12,3 +12,6 @@ primer:
     forward: CCTAYGGGDBGCWSCAG
     reverse: ATTAGADACCCBNGTAGTCC      
 
+$namespaces: 
+  edam: http://edamontology.org/
+

CWL/Workflows/remove_euk_prok_primer.workflow.cwl

@@ -5,16 +5,18 @@ label: Remove primers
 doc: remove specified primer in input sequences using cutadpt
 
 requirements:
-  - class: StepInputExpressionRequirement
-  - class: InlineJavascriptRequirement
-  - class: ScatterFeatureRequirement
-  - class: MultipleInputFeatureRequirement
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+  ScatterFeatureRequirement: {}
+  MultipleInputFeatureRequirement: {}
+  SchemaDefRequirement:
+    types:
+      - $import: ../primer-pair.yml
 
 inputs:
   sequences:
     type: File
-    format:
-      - fasta
+    format: edam:formate_1929  # FASTA
   primer:
     doc: Euk and Prokaryote primer
     type:
@@ -23,24 +25,10 @@ inputs:
       fields:
         - name: eukaryote
           doc: Eukaryote primer pair
-          type:
-            type: record
-            name: direction
-            fields:
-              - name: forward
-                type: string
-              - name: reverse
-                type: string
+          type: ../primer_pair.yml#primer_pair
         - name: prokaryote
           doc: Prokaryote primer pair
-          type:
-            name: direction
-            type: record
-            fields:
-              - name: forward
-                type: string
-              - name: reverse
-                type: string
+          type: ../primer_pair.yml#primer_pair
   error:
     type: string?
     default: "0.06"
@@ -70,7 +58,7 @@ steps:
        valueFrom: ^$(self.eukaryote.forward)
      a: 
        source: primer
-       valueFrom: $(self.eukaryote.reverse + '$') 
+       valueFrom: $(self.eukaryote.reverse)'$'
      trimmed-only: 
        default: true   
      error: error

CWL/Workflows/tap.dev.job.cwl

@@ -3,18 +3,26 @@ unite:
   path: /usr/local/share/db/UNITEv6_sh_dynamic_s.fasta
   # ../Data/Inputs/sequences.all.fasta
   # /usr/local/share/db/UNITE*.fasta
-  format: fasta
+  format: edam:format_1929  # fasta
 silva:
   class: File
   path: /usr/local/share/db/SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta
   # ../Data/Inputs/sequences.all.fasta
   # /usr/local/share/db/SILVA*.fasta
-  format: fasta
+  format: edam:format_1929  # fasta
 files:
-  - forward: ../Data/Inputs/samples_R1.fastq.gz
-    reverse: ../Data/Inputs/samples_R2.fastq.gz
-  - forward: ../Data/Inputs/samples_R1.fastq.gz
-    reverse: ../Data/Inputs/samples_R2.fastq.gz
+  - forward:
+      class: File
+      path: ../Data/Inputs/samples_R1.fastq.gz
+    reverse:
+      class: File
+      path: ../Data/Inputs/samples_R2.fastq.gz
+  - forward:
+      class: File
+      path: ../Data/Inputs/samples_R1.fastq.gz
+    reverse:
+      class: File
+      path: ../Data/Inputs/samples_R2.fastq.gz
 
 primer: 
   eukaryote:
@@ -28,7 +36,7 @@ mate_pair:
   forward:  
     class: File
     path: ../Data/Inputs/samples_R1.fastq.gz
-    format: fastq/gz
+    format: fastq.gz
   reverse:  
     class: File
     path: ../Data/Inputs/samples_R2.fastq.gz 

CWL/mate_pair.yml

@@ -0,0 +1,5 @@
+type: record
+name: mate_pair
+fields:
+  forward: File
+  reverse: File

CWL/primer_pair.yml

@@ -0,0 +1,5 @@
+type: record
+name: primer_pair
+fields:
+  forward: string
+  reverse: string