User: Michael R. Crusoe

Reputation:
1,010
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:
2 days, 19 hours ago
Joined:
5 years, 11 months ago
Email:
m*************@gmail.com

Posts by Michael R. Crusoe

<prev • 152 results • page 1 of 16 • next >
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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: '{"_": $(inputs)}' entryname: inputs.json ...
written 9 days ago by Michael R. Crusoe1.0k
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Answer: A: [cwl] referencing to list of paths in an array of files or direcories
... Hello grange, Since you're embedding your own code, you can get a JSON dump of the Directory object and walk over the "listing" attribute to extract the paths you need. Try `inpfiles=$(inputs.inpfiles)` in the Python block ...
written 9 days 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 18 days 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 18 days 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 18 days 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 4 weeks 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 4 weeks ago by Michael R. Crusoe1.0k
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Comment: C: Staging subdirectories in CWL
... Yes, this is possible, here's the tutorial for `InitialWorkDirRequirement`: http://www.commonwl.org/user_guide/15-staging/ I think you are asking to create one or more directories to enclose each sample? If you could be more specific about what you need to do, that would help us help you :-) Here ...
written 5 weeks ago by Michael R. Crusoe1.0k
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Comment: C: CommandLineTool doesn't finish
... FYI: `InlineJavascriptRequirement` is not needed for plain CWL parameter references like `$(runtime.outdir)` or `$(inputs.foo)`. See https://www.commonwl.org/v1.0/CommandLineTool.html#Parameter_references & http://www.commonwl.org/user_guide/06-params/ ...
written 5 weeks ago by Michael R. Crusoe1.0k
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Answer: A: How do I specify the elements of an array of output files?
... Hello @biokcb, I think you have the right approach. Maybe your `split_file.sh` script isn't outputting to the correct location? `glob` is checking the current working directory for the specified patterns. If you need to pass a path to your script to tell it where to put its outputs you can use `$(r ...
written 5 weeks ago by Michael R. Crusoe1.0k

Latest awards to Michael R. Crusoe

Guru 9 days ago, received more than 100 upvotes.
Scholar 9 days ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 18 days ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 6 weeks ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 12 weeks ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 7 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 8 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 8 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 8 months ago, created an answer that has been accepted. For A: Using the Directory type in Common Workflow Language
Scholar 12 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Centurion 12 months ago, created 100 posts.
Scholar 12 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 13 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 14 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 14 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 14 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 14 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 14 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 15 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 15 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Supporter 15 months ago, voted at least 25 times.

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