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Commit 9a5c0597 authored by Mattia Mancini's avatar Mattia Mancini
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Add cwl workflow specification

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Pipeline #33324 passed
cwlVersion: v1.2
class: Workflow
requirements:
- class: ScatterFeatureRequirement
inputs:
- id: surls
type: string[]
- id: samples_size
type: float?
doc: Sample sizes in seconds
- id: averaging_window
type: float?
doc: Averaging window in seconds
outputs:
- id: metadata_json
type:
type: array
items:
type: array
items: File
outputSource:
- generate_previews/metadata_json
- id: fits_files
type:
type: array
items:
type: array
items: File
outputSource:
- generate_previews/fits_files
- id: preview_png
type:
type: array
items:
type: array
items: File
outputSource:
- generate_previews/preview_png
steps:
- id: fetch_data
run: ./steps/fetch_data.cwl
in:
- id: surl_link
source: surls
out:
- id: beamformed_file
scatter:
- surl_link
- id: generate_previews
run: ./steps/extract_previews.cwl
in:
- id: dynspec_dataset
source: fetch_data/beamformed_file
- id: averaging_window
source: averaging_window
- id: samples_size
source: samples_size
scatter:
- dynspec_dataset
out:
- id: fits_files
- id: metadata_json
- id: preview_png
cwlVersion: v1.2
class: CommandLineTool
hints:
- class: DockerRequirement
dockerPull: git.astron.nl:5000/ldv/scintillation_pipeline
requirements:
- class: NetworkAccess
networkAccess: true
baseCommand:
- scintillation_utils.py
arguments:
- out
inputs:
- id: dynspec_dataset
type: File
inputBinding:
position: -1
- id: samples_size
type: float?
doc: Sample sizes in seconds
default: 3600
inputBinding:
prefix: --samples_size
- id: averaging_window
type: float?
doc: Averaging window in seconds
default: 1
inputBinding:
prefix: --averaging_window
outputs:
- id: metadata_json
type: File[]
outputBinding:
glob: out/*.json
- id: fits_files
type: File[]
outputBinding:
glob: out/*.fits
- id: preview_png
type: File[]
outputBinding:
glob: out/*.png
\ No newline at end of file
id: fetchdata
label: fetch_data
class: CommandLineTool
cwlVersion: v1.2
inputs:
- id: surl_link
type: string
inputBinding:
position: 0
outputs:
- id: beamformed_file
type: File
outputBinding:
glob: out/*.h5
secondaryFiles:
- pattern: '$(self.nameroot).raw'
required: True
baseCommand:
- 'bash'
- 'fetch.sh'
doc: 'Untar a compressed file'
requirements:
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
listing:
- entryname: 'fetch.sh'
entry: |
#!/bin/bash
mkdir out
cd out
echo "Downloading $1"
gfal-copy $1 ..
tar -xvf ../*.tar
\ No newline at end of file
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