User: Michael R. Crusoe

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Common Workflow Language project
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https://orcid.org/0000...
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biocrusoe
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Last seen:
3 weeks, 5 days ago
Joined:
7 years, 6 months ago
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Posts by Michael R. Crusoe

<prev • 215 results • page 1 of 22 • next >
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News: CWL user support moving to https://cwl.discourse.group/; many thanks to Biostars for over 4 years of support!
... Dear Biostars, Thank you for over 4 years of supporting the Common Workflow Language project and its users. As CWL has grown beyond bioinformatics, we have moved to another forum site. Anyone with any question related to CWL, bio* related or not, is welcome to ask and answer questions (along with ...
thanks news cwl written 4 months ago by Michael R. Crusoe1.8k
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Comment: C: CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
... `/scripts/runfolder-check.sh: line 31: /scripts/runfolder-check.sh.dev.log: Read-only file system` The script is trying to write a log file in its directory. It should either use `$TMPDIR`, or write the log to a user specified path. ...
written 4 months ago by Michael R. Crusoe1.8k
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Answer: A: CWL: Does cwltool support to download both input file and its secondaryFiles rem
... Hello Linda, and thank you for your posting, Yes, this should work, but use `location` instead of `path` when specifying using URLs ref_file: location: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa ...
written 4 months ago by Michael R. Crusoe1.8k
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Answer: A: secondaryFiles where nameroot differs
... Hello Peter vH, I think there are two separate challenges here: 1) describing a File with secondaryFiles that don't share anything in common name-wise and 2) staging a File and its secondaries inside a named directory For (1), on can provide the plain name for each of the desired secondaryFiles ...
written 5 months ago by Michael R. Crusoe1.8k
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Comment: C: Input specific output filenames
... A simpler variation of the `stdout`: stdout: $(inputs.reads.nameroot)_console_log.txt ...
written 5 months ago by Michael R. Crusoe1.8k
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Answer: A: how do I default to /dev/null in CommandLineTool
... Another solution, using an empty file: cwlVersion: v1.0 class: CommandLineTool inputs: optional_file: type: File default: class: File size: 0 basename: empty contents: "" inputBinding: {} baseCommand: [ ...
written 5 months ago by Michael R. Crusoe1.8k
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Answer: A: how do I default to /dev/null in CommandLineTool
... Hello Azat Badretdin, You'll need to use a [CWL Javascript Expression](https://www.commonwl.org/user_guide/13-expressions/index.html) Here is an example: cwlVersion: v1.0 class: CommandLineTool requirements: InlineJavascriptRequirement: {} inputs: optional_fi ...
written 5 months ago by Michael R. Crusoe1.8k
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Comment: C: Is there a schema for CWL inputs/job files?
... Hey Karl. Yep, you are very close to a valid schema salad representation for the `1st_tool.cwl`'s input section. You'll need to add `- $import: "schema_salad/metaschema/metaschema_base.yml"` to the beginning of the document and leave out the `Inputs` section, then the following will work: $ sc ...
written 6 months ago by Michael R. Crusoe1.8k
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Comment: C: cwltool "invalid field" error messages
... FYI, this sounds like an error in `cwltool`, I am investigating ...
written 6 months ago by Michael R. Crusoe1.8k
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Comment: C: Add an item from input to an output array in CWL
... Congratulations on your pending thesis! Yes, no rush. Any contribution is appreciated! ...
written 6 months ago by Michael R. Crusoe1.8k

Latest awards to Michael R. Crusoe

Appreciated 27 days ago, created a post with more than 5 votes. For A: Output going to stdout?
Scholar 12 weeks 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)?
Voter 8 months ago, voted more than 100 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Appreciated 10 months ago, created a post with more than 5 votes. For A: Output going to stdout?
Scholar 10 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)?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Commentator 11 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
Scholar 12 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
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: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
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)?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values

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