add concat step

Former-commit-id: 7edd5620 [formerly 0f102300]
Former-commit-id: acd2618b
Former-commit-id: 1acbf4c4

steps/bulk_rename.cwl

@@ -15,12 +15,11 @@ inputs:
     type: string
   - id: file_suffix
     type: string?
-    default: log
 outputs:
   - id: output
-    type: File
+    type: 'File[]'
     outputBinding:
-      glob: "$(inputs.file_prefix).$(inputs.file_suffix)"
+      glob: "tmp/$(inputs.file_prefix)*"
 label: bulk_rename
 requirements:
   - class: InitialWorkDirRequirement
@@ -32,6 +31,9 @@ requirements:
           FILE_LIST=("\${@}")
           FILE_PREFIX=$(inputs.file_prefix)
           FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)
-          cat "\${FILE_LIST[@]}" > "\$FILE_PREFIX.\$FILE_SUFFIX"
+          mkdir tmp
+          for i in "\${!FILE_LIST[@]}"; do 
+            cp "\${FILE_LIST[\$i]}" "tmp/\${FILE_PREFIX}_\${i}\${FILE_SUFFIX}"
+          done
         writable: false
-  - class: InlineJavascriptRequirement
+  - class: InlineJavascriptRequirement
\ No newline at end of file

steps/concatenate_files.cwl

+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+id: bulk_rename
+baseCommand:
+  - bash 
+  - bulk_rename.sh
+inputs:
+  - id: file_list
+    type: 'File[]'
+    inputBinding:
+      position: 0
+  - id: file_prefix
+    type: string
+  - id: file_suffix
+    type: string?
+    default: log
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: "$(inputs.file_prefix).$(inputs.file_suffix)"
+label: bulk_rename
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: bulk_rename.sh
+        entry: |
+          #!/bin/bash
+          set -e
+          FILE_LIST=("\${@}")
+          FILE_PREFIX=$(inputs.file_prefix)
+          FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)
+          cat "\${FILE_LIST[@]}" > "\$FILE_PREFIX.\$FILE_SUFFIX"
+        writable: false
+  - class: InlineJavascriptRequirement

workflows/HBA_calibrator.cwl

 class: Workflow
 cwlVersion: v1.0
-id: _h_b_a_calibrator
+id: HBA_calibrator
 label: HBA_calibrator
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
@@ -73,7 +73,7 @@ inputs:
     'sbg:y': -500
   - id: maxStddev
     type: float?
-    default: -1
+    default: -1.0
     'sbg:x': -1000
     'sbg:y': -400
   - id: solutions2transfer
@@ -160,7 +160,7 @@ inputs:
     'sbg:y': 1200
   - id: max_separation_arcmin
     type: float?
-    default: 1
+    default: 1.0
     'sbg:x': -1000
     'sbg:y': 1300
   - id: calibrator_path_skymodel
@@ -319,7 +319,7 @@ steps:
         default: dppp_prep_cal
     out:
       - id: output
-    run: ./../steps/bulk_rename.cwl
+    run: ./../steps/concatenate_files.cwl
     label: concat_logfiles
     'sbg:x': 500
     'sbg:y': 1000