User: Michael R. Crusoe

Reputation:
1,080
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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:
5 days, 10 hours ago
Joined:
6 years, 3 months ago
Email:
m*************@gmail.com

Posts by Michael R. Crusoe

<prev • 161 results • page 1 of 17 • next >
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Comment: C: CWL: How to return int or string[] from CommandLineTool?
... Thanks, I've fixed my answer and added a version without Javscript ...
written 8 days ago by Michael R. Crusoe1.1k
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Answer: A: CWL: How to return int or string[] from CommandLineTool?
... Hello uagrif, The newline that `echo` outputs is the cause, so pass `-n`: > -n do not output the trailing newline #!/usr/bin/env cwl-runner class: CommandLineTool cwlVersion: "v1.0" requirements: InlineJavascriptRequirement: {} baseCommand: [bash, -c, "echo -n ...
written 9 days ago by Michael R. Crusoe1.1k
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Answer: A: cwltool issue using SoftwareRequirement
... Hello h.mon, When I've had this issue in the past I've fixed it by running `cwltool` inside a Python 2.7 virtualenv. But this is a bug, so I've opened an issue at https://github.com/common-workflow-language/cwltool/issues/954 to track it. Thanks! ...
written 24 days ago by Michael R. Crusoe1.1k
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Comment: C: best practice for renaming file in CWL workflow
... `cwlexec` does support `InlineJavascriptRequirement`s so there is no compatibility issue with the asker's proposal. If you've experienced a problem with `cwlexec` then that should be reported to https://github.com/IBMSpectrumComputing/cwlexec/issues?q=is%3Aopen+is%3Aissue and to your IBM support co ...
written 25 days ago by Michael R. Crusoe1.1k
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Answer: A: best practice for renaming file in CWL workflow
... Hello ionox0, That is acceptable way to rename, yes. However, `**` is not part of the POSIX glob definition, so you'll need to amend that. Perhaps the following simplification works with your tool? processed_fastq_1: type: File outputBinding: glob: */$(inputs.fastq1 ...
written 25 days ago by Michael R. Crusoe1.1k
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Answer: A: possible to show job names in toil stats command using cwl workflow
... Thank you ionox0, your PR to Toil to fix this has been merged: https://github.com/DataBiosphere/toil/pull/2397 ...
written 5 weeks ago by Michael R. Crusoe1.1k
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Answer: A: Possible to combine inputs using valueFrom for scatter
... Hello ionox0, Yes, this is possible. Just wire up the other inputs to non-existent names and reference them from your expression inputs: input_one: Directory input_two: Directory steps: a_step: run: ../../cwl_tools/noise/calculate_noise.cwl ...
written 10 weeks ago by Michael R. Crusoe1.1k
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Comment: C: CWL Error Empty Scatter
... For `A` you can accomplish this using `linkMerge: merge_flattened`: steps: stepname: run: scatter: [A, B] scatterMethod: dotproduct in: A: source: arrayC, arrayD linkMerge: merge_flattened ...
written 10 weeks ago by Michael R. Crusoe1.1k
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Comment: C: CWL Error Empty Scatter
... Hello HL, thank you for your question. `$( 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 10 weeks ago by Michael R. Crusoe1.1k
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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 4 months ago by Michael R. Crusoe1.1k

Latest awards to Michael R. Crusoe

Scholar 23 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)?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Guru 4 months ago, received more than 100 upvotes.
Scholar 4 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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: Example cwl workflow (for v1.0)?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 5 months 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 11 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 12 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 12 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 12 months ago, created an answer that has been accepted. For A: Using the Directory type in Common Workflow Language
Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Centurion 16 months ago, created 100 posts.
Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 18 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 18 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 18 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 18 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?

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