Add ldv workflow

steps/compress.cwl

+id: compress
+label: compress
+class: CommandLineTool
+cwlVersion: v1.2
+inputs: 
+  - id: directory
+    type: Directory
+outputs: 
+  - id: compressed
+    type: File
+    outputBinding:
+      glob: 'out/*.tar'
+baseCommand: 
+ - 'bash'
+ - 'tar.sh'
+doc: 'Create archive from directory'
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.directory)
+      - entryname: 'tar.sh' 
+        entry: |
+          #!/bin/bash
+          mkdir out
+          tar -h -cvf out/$(inputs.directory.basename).tar $(inputs.directory.basename) 

steps/fetch_data.cwl

+id: fetchdata
+label: fetch_data
+class: CommandLineTool
+cwlVersion: v1.2
+inputs: 
+  - id: surl_link
+    type: string
+    inputBinding:
+      position: 0
+    
+outputs: 
+  - id: uncompressed
+    type: Directory
+    outputBinding:
+      glob: 'out/*'
+baseCommand: 
+  - 'bash'
+  - 'fetch.sh'
+doc: 'Fetch a file from surl and uncompresses it'
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'fetch.sh' 
+        entry: |
+          #!/bin/bash
+          mkdir out
+          cd out
+          turl=`echo $1 | awk '{gsub("srm://srm.grid.sara.nl[:0-9]*","gsiftp://gridftp.grid.sara.nl"); print}'`
+          echo "Downloading $turl"
+          globus-url-copy $turl - | tar -xvf -
+
+    

steps/fetch_file.cwl

+id: fetchfile
+label: fetch_file
+class: CommandLineTool
+cwlVersion: v1.2
+inputs: 
+  - id: surl_link
+    type: string
+    inputBinding:
+      position: 0
+    
+outputs: 
+  - id: downloaded
+    type: File
+    outputBinding:
+      glob: 'out/*'
+baseCommand: 
+ - 'bash'
+ - 'fetch.sh'
+doc: 'Fetch a file from surl'
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'fetch.sh' 
+        entry: |
+          #!/bin/bash
+          mkdir out
+          cd out
+          turl=`echo $1 | awk '{gsub("srm://srm.grid.sara.nl[:0-9]*","gsiftp://gridftp.grid.sara.nl"); print}'`
+          filename=`echo $1 | awk '{sub(".*/", "", $1); print $0}'`
+          echo "Downloading $turl"
+          globus-url-copy $turl file://$PWD/$filename
+
+    

steps/list_directory.cwl

+id: listdirectory
+label: list_directory
+class: ExpressionTool
+
+cwlVersion: v1.2
+inputs:
+  - id: input
+    type: Directory
+    loadListing: shallow_listing
+outputs:
+  - id: output
+    type: Directory[]
+
+expression: |
+  ${
+    return {'output': inputs.input.listing}
+  }
+
+
+requirements:
+  - class: InlineJavascriptRequirement

workflows/ldv_prefactor_calibrator.cwl

+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+- class: ScatterFeatureRequirement
+- class: SubworkflowFeatureRequirement
+
+inputs:
+- id: surls
+  type: string[]
+
+outputs:
+- id: solutions
+  type: File
+  outputSource:
+  - prefactor_calibrator/solutions
+- id: summary
+  type: File
+  outputSource:
+  - prefactor_calibrator/summary
+- id: inspection_plots
+  type: File
+  outputSource:
+  - compress_inspection_plots/compressed
+- id: log_files
+  type: File
+  outputSource:
+  - compress_logs/compressed
+steps:
+- id: fetch_data
+  in:
+  - id: surl_link
+    source: surls
+  scatter: surl_link
+  run: ../steps/fetch_data.cwl
+  out:
+  - id: uncompressed
+- id: prefactor_calibrator
+  in:
+  - id: msin
+    source: fetch_data/uncompressed
+  run: HBA_calibrator.cwl
+  out:
+  - id: solutions
+  - id: summary
+  - id: inspection_plots
+  - id: log_files
+- id: compress_inspection_plots
+  in: 
+  - id: directory
+    source: prefactor_calibrator/inspection_plots
+  out:
+  - id: compressed
+  run: ../steps/compress.cwl
+- id: compress_logs
+  in:
+  - id: directory
+    source: prefactor_calibrator/log_files
+  out:
+  - id: compressed
+  run: ../steps/compress.cwl
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workflows/ldv_prefactor_target.cwl

+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  - class: ScatterFeatureRequirement
+  - class: SubworkflowFeatureRequirement
+
+inputs:
+  - id: surls
+    type: string[]
+  - id: solutions
+    type: string
+  - id: avg_timeresolution_concat
+    type: int?
+    default: 4
+  - id: avg_freqresolution_concat
+    type: string?
+    default: 48.82kHz
+
+outputs:
+  - id: cal_solutions
+    type: File
+    outputSource:
+    - prefactor_target/solutions
+  - id: summary
+    type: File
+    outputSource:
+    - prefactor_target/summary
+  - id: calibrated_data
+    type: File[]
+    outputSource:
+    - compress_calibrated_data/compressed
+  - id: inspection_plots
+    type: File
+    outputSource:
+    - compress_inspection_plots/compressed
+  - id: log_files
+    type: File
+    outputSource:
+    - compress_logs/compressed
+steps:
+  - id: fetch_data
+    in:
+    - id: surl_link
+      source: surls
+    scatter: surl_link
+    run: ../steps/fetch_data.cwl
+    out:
+    - id: uncompressed
+  - id: fetch_solutions
+    in: 
+    - id: surl_link
+      source: solutions
+    run: ../steps/fetch_file.cwl
+    out:
+    - id: downloaded
+  - id: prefactor_target
+    in:
+    - id: msin
+      source: fetch_data/uncompressed
+    - id: cal_solutions
+      source: fetch_solutions/downloaded
+    - id: avg_timeresolution_concat
+      source: avg_timeresolution_concat
+    - id: avg_freqresolution_concat
+      source: avg_freqresolution_concat
+    run: HBA_target.cwl
+    out:
+    - id: solutions
+    - id: calibrated_data
+    - id: summary
+    - id: inspection_plots
+    - id: log_files
+  - id: compress_inspection_plots
+    in: 
+    - id: directory
+      source: prefactor_target/inspection_plots
+    out:
+    - id: compressed
+    run: ../steps/compress.cwl
+
+  - id: split_calibrated_data
+    in: 
+    - id: input
+      source: prefactor_target/calibrated_data
+    out:
+    - id: output
+    run: ../steps/list_directory.cwl
+  - id: compress_calibrated_data
+    in:
+    - id: directory
+      source: split_calibrated_data/output
+    out:
+    - id: compressed
+    run: ../steps/compress.cwl
+    scatter: directory
+  - id: compress_logs
+    in:
+    - id: directory
+      source: prefactor_target/log_files
+    out:
+    - id: compressed
+    run: ../steps/compress.cwl
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