User: Michael R. Crusoe

Reputation:
800
Status:
Trusted
Location:
currently based out of Vilnius, Lithuania / Common Workflow Language project
Website:
https://orcid.org/0000...
Twitter:
biocrusoe
Scholar ID:
Google Scholar Page
Last seen:
6 days, 21 hours ago
Joined:
5 years, 8 months ago
Email:
m*************@gmail.com

Posts by Michael R. Crusoe

<prev • 130 results • page 1 of 13 • next >
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Answer: A: CWL: Is there a way to only pass certain fields from a `record` type to a step?
... You almost have it: steps: step_2: in: SM: source: samples valueFrom: ${ return self.map(function(x) { return x.SM }) ...
written 8 days ago by Michael R. Crusoe800
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Answer: A: Gather sorting by parameter in the metadata of input file
... 1. Expose the frequency as a separate output. 2. Write an ExpressionTool to batch and sort the arrays of files and frequencies ...
written 15 days ago by Michael R. Crusoe800
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Answer: A: CWL: Specify type of input file
... Hello sc35 and thank you for your question. The answer depends on what you mean by "insist" :-) The `format` field can be used to signal which File format you expect: http://www.commonwl.org/user_guide/16-file-formats/ But validation (beyond matching the format values) is up to the workflow engine ...
written 9 weeks ago by Michael R. Crusoe800
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Answer: A: cwl: unrecognized extension field, $schemas section
... Hello @ninsch3000 This is a known false warning: https://github.com/common-workflow-language/cwltool/issues/623 You can ignore it; sorry! ...
written 11 weeks ago by Michael R. Crusoe800
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Answer: A: Output files in the input directory
... Hello thomas.e, This is very much supported by CWL! See http://www.commonwl.org/user_guide/15-staging/ to learn how to stage your input files into the working directory. Cheers, ...
written 4 months ago by Michael R. Crusoe800
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Comment: C: cwl: how to add optional input as one element or as array of elements ?
... Then the second option I gave should work for you as it prefixed "--opt" prior to each item. inputs: opt: type: - "null" - type: array items: File inputBinding: prefix: --opt give "--opt file2 --opt file2" while inp ...
written 4 months ago by Michael R. Crusoe800
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Answer: A: CWL: Gathering outputs in folders.
... Hello lon.lightly, The best thing would be to modify the script so that the user can specify the location (if not the filename) of "B.txt". One workaround involves the `InitialWorkDirRequirement` but in testing it using nested directories I found a bug in the reference CWL runner: https://github.c ...
written 4 months ago by Michael R. Crusoe800
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Comment: C: CWL: Make Enum optional (CommandInputEnumSchema)
... type: - "null" - type: array items: type: enum symbols: [none, apply, calculate] Yes, as you found, it is easier when we give names to our custom types ...
written 4 months ago by Michael R. Crusoe800
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Answer: A: CWL: Make Enum optional (CommandInputEnumSchema)
... From https://github.com/common-workflow-language/common-workflow-language/issues/392 type: - "null" - type: enum symbols: [none, apply, calculate] Or give it a name: https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/master/tools/InterProScan5.21-60.cwl#L38 ...
written 4 months ago by Michael R. Crusoe800
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Answer: A: CWL 'glob' field not capturing files
... Hello eduardo, Sorry for the confusion, the fact that `outputBinding` is allowed here doesn't make much sense and I've started the process to change/remove that: https://github.com/common-workflow-language/common-workflow-language/issues/543 You'll either need another tool to parse the `sss/cwl_ou ...
written 5 months ago by Michael R. Crusoe800

Latest awards to Michael R. Crusoe

Scholar 4 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 5 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 5 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 5 months ago, created an answer that has been accepted. For A: Using the Directory type in Common Workflow Language
Scholar 9 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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Scholar 9 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
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Scholar 11 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 11 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 11 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
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