User: Michael R. Crusoe

Reputation:
1,200
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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:
3 weeks, 2 days ago
Joined:
6 years, 6 months ago
Email:
m*************@gmail.com

Posts by Michael R. Crusoe

<prev • 175 results • page 1 of 18 • next >
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Comment: C: CWL Workflow removing input files
... Hello Tom, Which CWL runner are you using, and which version is it? Do your CWL descriptions use the `DockerRequirement`? Can you share a link to view your CWL descriptions? ...
written 23 days ago by Michael R. Crusoe1.2k
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Answer: C: CWL with R returns empty output directory with "Final process status is success"
... Hello @a.james, thank you for your question. Are you sure that your tool is outputting to the directory? I made a self contained version that does seem to work: cwlVersion: v1.0 class: CommandLineTool requirements: InlineJavascriptRequirement: {} InitialWorkDirRequirement ...
written 23 days ago by Michael R. Crusoe1.2k
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Comment: C: CWL can't find tools it's supposed to run
... This is a fairly common user experience and we want CWL to be useful even before one has containerized all the steps; therefore we should document how to deal with this situation. ...
written 25 days ago by Michael R. Crusoe1.2k
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Comment: C: CWL can't find tools it's supposed to run
... We reset HOME so that may be a challenge. What if you use a Python Virtualenv? ...
written 25 days ago by Michael R. Crusoe1.2k
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Comment: C: Staging subdirectories in CWL
... env PATH=`pwd`:$PATH will have no effect for most `cwl-runner`s. If you're using `cwltool` try the following: env PATH=`pwd`:$PATH cwltool --preserve-environment PATH io-redirection-cmd.cwl --in_file nicholas.txt --out_dir abc or env PATH=`pwd`:$PATH cwltool --preserve-entire-environ ...
written 25 days ago by Michael R. Crusoe1.2k
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Answer: A: CWL can't find tools it's supposed to run
... Hello Tom, thank you for your question. I presume that you're not using the `DockerRequirement` yet and want to run local software. If you've installed the Python libraries in a virtualenv or done a `--user` install then you'll need to pass in a few environment variables when using the CWL reference ...
written 25 days ago by Michael R. Crusoe1.2k
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Comment: C: CWL: How to refer to input or scattered value of a step
... Hello jshelton; thank you for your question, (I think it should maybe be a new question on its own and not a "answer" to the original question above?) Can you share a link to which bedtools CWL description you are using? ...
written 6 weeks ago by Michael R. Crusoe1.2k
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Comment: C: load/parse cwl using Java
... Probably best to make an issue at https://github.com/common-workflow-language/cwlavro/issues/new and tag https://github.com/denis-yuen to request his assistance ...
written 8 weeks ago by Michael R. Crusoe1.2k
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Comment: C: How to specify enum symbols in record type definition?
... With the newly released version `1.0.20181201184214` of `cwltool` the above is now simpler: cwlVersion: v1.0 class: CommandLineTool requirements: SchemaDefRequirement: types: - name: vcf2maf_params type: record fields: speci ...
written 11 weeks ago by Michael R. Crusoe1.2k
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Comment: C: best practice for renaming file in CWL workflow
... Thanks! I've added your suggestion to https://github.com/common-workflow-language/common-workflow-language/issues/668#issuecomment-443176439 ...
written 11 weeks ago by Michael R. Crusoe1.2k

Latest awards to Michael R. Crusoe

Scholar 25 days ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Teacher 10 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)?
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Commentator 6 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
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Scholar 7 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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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)
Scholar 15 months ago, created an answer that has been accepted. For A: Using the Directory type in Common Workflow Language
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