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class: CommandLineTool
cwlVersion: v1.2
id: subtract_with_wsclean
label: Subtract with WSClean
doc: This step uses WSClean to subtract visibilities corresponding to model images.
baseCommand: python3
inputs:
- id: msin
type: Directory
doc: MeasurementSet for source subtraction.
inputBinding:
prefix: "--mslist"
position: 1
- id: model_image_folder
type: Directory
doc: Directory containing 1.2" (or optionally other resolution) model images.
inputBinding:
prefix: "--model_image_folder"
position: 2
- id: facet_regions
type: File
doc: The DS9 region file that defines the facets for prediction.
inputBinding:
prefix: "--facets_predict"
position: 3
- id: h5parm
type: File
doc: The HDF5 solution file containing the solutions for prediction.
inputBinding:
prefix: "--h5parm_predict"
position: 4
- id: lofar_helpers
type: Directory
doc: LOFAR helpers directory.
- id: copy_to_local_scratch
type: boolean?
default: false
inputBinding:
prefix: "--copy_to_local_scratch"
position: 5
separate: false
doc: Specific option for using --bypass-file-store on the Spider cluster to run predict and subtract on local scratch.
- id: ncpu
type: int?
doc: Number of cores to use during the subtract.
default: 16
outputs:
- id: logfile
type: File[]
doc: Log files from current step.
outputBinding:
glob: subtract_fov*.log
- id: subtracted_ms
type: Directory
doc: MS subtracted data
outputBinding:
glob: subfov_*.ms
arguments:
- $( inputs.lofar_helpers.path + '/subtract/subtract_with_wsclean.py' )
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing: >
${
// Set 'writable' on the "msin" entry only if copy_to_local_scratch is true.
let stagedListing = [
{ entry: inputs.msin },
{ entry: inputs.model_image_folder },
{ entry: inputs.facet_regions },
{ entry: inputs.h5parm }
];
if (!inputs.copy_to_local_scratch) {
stagedListing[0].writable = true;
}
return stagedListing;
}
hints:
- class: DockerRequirement
dockerPull: vlbi-cwl
- class: ResourceRequirement
coresMin: $(inputs.ncpu)
stdout: subtract_fov.log
stderr: subtract_fov_err.log