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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Joined:
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Posts by Michael R. Crusoe

<prev • 215 results • page 1 of 22 • next >
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Answer: A: CWL: Min and max for tool input values (float,int)
... Constrains on input values has been proposed, but not yet implemented nor added to the CWL standards yet: https://github.com/common-workflow-language/common-workflow-language/issues/764 ...
written 5 months ago by Michael R. Crusoe1.8k
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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 12 months ago by Michael R. Crusoe1.8k • updated 7 months ago by ATpoint40k
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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 12 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 12 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 13 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 13 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 13 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 13 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 14 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 14 months ago by Michael R. Crusoe1.8k

Latest awards to Michael R. Crusoe

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Appreciated 9 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)?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Voter 16 months ago, voted more than 100 times.
Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Appreciated 18 months ago, created a post with more than 5 votes. For A: Output going to stdout?
Scholar 18 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 19 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Commentator 19 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
Scholar 20 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 21 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 22 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 22 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 2.0 years ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish

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