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ms_concat.cwl
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Marcel Loose authored
Some of the inline scripts (bash or python) have names like "script.py", which is not very helpful for debugging. Renamed the scripts for those workflows that contained either script.py or script.sh. Former-commit-id: 05c75d3e
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ms_concat.cwl 1.75 KiB
class: CommandLineTool
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: ms_concat
baseCommand:
- /bin/bash
- ms_concat.sh
inputs:
- default: 50
id: min_length
type: int?
inputBinding:
position: 0
prefix: '--min_length'
doc: Minimum amount of subbands to concatenate in frequency.
- id: overhead
type: float?
default: 0.8
inputBinding:
position: 0
prefix: '--overhead'
doc: |
Only use this fraction of the available memory for deriving the amount
of data to be concatenated.
- id: msin
type: 'Directory[]'
- default: out.MS
id: msout
type: string
inputBinding:
position: 2
outputs:
- id: concat_meta_ms
type: 'Directory'
outputBinding:
glob: |
workdir/$(inputs.msout)_[0-9*]
- id: concat_additional_ms
type: 'Directory'
outputBinding:
glob: |
workdir/$(inputs.msout)_*_CONCAT
- id: ms_outs
type: 'Directory[]'
outputBinding:
glob: 'workdir/out_*'
- id: logfile
type: File
outputBinding:
glob: ms_concat.log
label: ms_concat
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor3-cwl'
requirements:
- class: ShellCommandRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
- entryname: ms_concat.sh
entry: |
#!/bin/bash
directories=\$(ls -d out_*)
#echo \$directories
mkdir -pv workdir
cp -r \$directories workdir/. && cd workdir
concat_MS_CWL.py \$1 \$2 \$3 \$4 \$directories \$5
- class: InplaceUpdateRequirement inplaceUpdate: true
- class: InlineJavascriptRequirement
stdout: ms_concat.log
stderr: ms_concat_err.log