User: Michael R. Crusoe

Reputation:
1,040
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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:
1 day ago
Joined:
6 years, 1 month ago
Email:
m*************@gmail.com

Posts by Michael R. Crusoe

<prev • 155 results • page 1 of 16 • next >
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Answer: A: Possible to combine inputs using valueFrom for scatter
... Hello ionox0, Yes, this is possible. Just wire up the other inputs to non-existent names and reference them from your expression inputs: input_one: Directory input_two: Directory steps: a_step: run: ../../cwl_tools/noise/calculate_noise.cwl ...
written 15 days ago by Michael R. Crusoe1.0k
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Comment: C: CWL Error Empty Scatter
... For `A` you can accomplish this using `linkMerge: merge_flattened`: steps: stepname: run: scatter: [A, B] scatterMethod: dotproduct in: A: source: arrayC, arrayD linkMerge: merge_flattened ...
written 15 days ago by Michael R. Crusoe1.0k
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Comment: C: CWL Error Empty Scatter
... Hello HL, thank you for your question. `$( return arrayC.concat(arrayD))` is not a valid expression. Did you mean `$( return inputs.arrayC.concat(inputs.arrayD))`? Can you provide a testable example so we can help you? ...
written 15 days ago by Michael R. Crusoe1.0k
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Comment: C: [cwl] referencing to list of paths in an array of files or direcories
... You can have it written to a file and then load json in the Python section requirements: InitialWorkDirRequirement: listing: - entry: '{"_": $(inputs)}' entryname: inputs.json ...
written 11 weeks ago by Michael R. Crusoe1.0k
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Answer: A: [cwl] referencing to list of paths in an array of files or direcories
... Hello grange, Since you're embedding your own code, you can get a JSON dump of the Directory object and walk over the "listing" attribute to extract the paths you need. Try `inpfiles=$(inputs.inpfiles)` in the Python block ...
written 11 weeks ago by Michael R. Crusoe1.0k
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Comment: C: change temp folder in cwl
... Hello roalva1, thank you for your question. Can you provide more information or context? ...
written 12 weeks ago by Michael R. Crusoe1.0k
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Answer: A: How does cwltool actually check file formats?
... Hello biokcb, good question. The CWL reference runner only checks the compatibility of the declared formats, it does not look into the files themselves. Other CWL implementations could choose to do file format verification, but are not required. You can read more about the format field in the CWL ...
written 12 weeks ago by Michael R. Crusoe1.0k
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Comment: C: Is there a way to convert ["null", File] to File in CWL?
... Hello azat1b, can you give us more context as to what you're trying to do? ...
written 12 weeks ago by Michael R. Crusoe1.0k
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Comment: C: String concatenation for output
... FYI: It would be more correct if it was `baseCommand: fastqc_check.sh` and either a `DockerRequirement` and/or a `SoftwareRequirement` was used. ...
written 3 months ago by Michael R. Crusoe1.0k
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Comment: C: CommandLineTool doesn't finish
... Can you change your answer to reflect this? Thanks! ...
written 3 months ago by Michael R. Crusoe1.0k

Latest awards to Michael R. Crusoe

Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Guru 11 weeks ago, received more than 100 upvotes.
Scholar 11 weeks ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
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Scholar 10 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 10 months ago, created an answer that has been accepted. For A: Using the Directory type in Common Workflow Language
Scholar 14 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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Scholar 14 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
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Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 16 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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