User: Michael R. Crusoe

Reputation:
1,510
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Trusted
Location:
Common Workflow Language project
Website:
https://orcid.org/0000...
Twitter:
biocrusoe
Scholar ID:
Google Scholar Page
Last seen:
50 minutes ago
Joined:
6 years, 10 months ago
Email:
m*************@gmail.com

Posts by Michael R. Crusoe

<prev • 198 results • page 1 of 20 • next >
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Answer: A: Parse CWL to graph data structure or database?
... Hello mcpherson, That is exciting to hear about your plans! Did you explore using the RDF graph output from the CWL reference runner via `cwltool --print-rdf`? I'm also surprised that `cwl-utils` didn't seem useful to you all. It does take another recursive traversal to load everything, but once ...
written 2 days ago by Michael R. Crusoe1.5k
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Comment: C: CWL inputs autogenerator
... Quick note: looks like your tags got combined into a single tag :-) Maybe add commas? ...
written 2 days ago by Michael R. Crusoe1.5k
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Answer: A: CWL inputs autogenerator
... Hello waleed.a.osman, The CWL reference runner, `cwltool`, has a `--make-template` option that may be useful to you. Run it like this: `cwltool --make-template /path/to/cwl/description` and then customize the output with the desired parameters and file paths. ...
written 2 days ago by Michael R. Crusoe1.5k
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Comment: C: CWL :Append the ref input used in toolkit
... See also https://github.com/wtsi-hgi/gatk-cwl-generator ...
written 3 days ago by Michael R. Crusoe1.5k
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Comment: C: CWL :Append the ref input used in toolkit
... try: type: string[] inputBinding: prefix: -L ...
written 7 days ago by Michael R. Crusoe1.5k
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Answer: A: Rename file in CWL ExpressionTool?
... Hello alanh, Yes, you can rename files using an `ExpressionTool` in CWL. Change the `basename` property of the `File` objects. Here is a very complicated example: https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/cac44f2cf14110fde9951161c663c4525772f616/workflows/convert-to-v3-layout. ...
written 10 days ago by Michael R. Crusoe1.5k
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Answer: A: Rename file in CWL ExpressionTool?
... Hello alanh, Yes, you can rename files using an `ExpressionTool` in CWL. Change the `basename` property of the `File` objects. Here is a very complicated example: https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/cac44f2cf14110fde9951161c663c4525772f616/workflows/convert-to-v3-layout. ...
written 10 days ago by Michael R. Crusoe1.5k
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Answer: A: CWL :Append the ref input used in toolkit
... Hello lizhichao, For creating configuration files at runtime, please consult this part of the CWL User Guide: https://www.commonwl.org/user_guide/14-runtime/index.html ...
written 10 days ago by Michael R. Crusoe1.5k
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Answer: A: Is there a schema for CWL inputs/job files?
... Hello Karl, Yes, the `inputs` section of a CWL document is a schema for the input job object. ...
written 10 days ago by Michael R. Crusoe1.5k
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Comment: C: interesting behavior with grep
... You're in a situation where I would either recommend using a bash script or splitting into multiple `CommandLineTools` I take back my comment about `$(inputs.vcfs)`, I was thinking of something else :-) ...
written 24 days ago by Michael R. Crusoe1.5k

Latest awards to Michael R. Crusoe

Voter 7 days ago, voted more than 100 times.
Scholar 10 days ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Output going to stdout?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 9 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)?
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 3 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 4 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 6 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 6 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
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: Example cwl workflow (for v1.0)?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
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 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: Example cwl workflow (for v1.0)?

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