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:
5 days, 13 hours ago
Joined:
7 years, 2 months ago
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Posts by Michael R. Crusoe

<prev • 214 results • page 1 of 22 • next >
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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 14 days ago by Michael R. Crusoe1.7k
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100
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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 14 days ago by Michael R. Crusoe1.7k
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127
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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 weeks ago by Michael R. Crusoe1.7k
1
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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 weeks ago by Michael R. Crusoe1.7k
1
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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 7 weeks ago by Michael R. Crusoe1.7k
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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 7 weeks ago by Michael R. Crusoe1.7k
1
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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 9 weeks ago by Michael R. Crusoe1.7k
1
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Comment: C: cwltool "invalid field" error messages
... FYI, this sounds like an error in `cwltool`, I am investigating ...
written 11 weeks ago by Michael R. Crusoe1.7k
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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 11 weeks ago by Michael R. Crusoe1.7k
0
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3
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324
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3
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Comment: C: Parse CWL to graph data structure or database?
... Great summary mcpherson! Yes, we'd like to add more of the semantic processing to `parser_v1_N.py ` either automatically or via an external file that gets included at code generation time. Some aspects of the graph you'll have to leave slightly abstract until execution time: scattering can't be re ...
written 11 weeks ago by Michael R. Crusoe1.7k

Latest awards to Michael R. Crusoe

Teacher 11 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)?
Voter 4 months ago, voted more than 100 times.
Scholar 4 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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Appreciated 5 months ago, created a post with more than 5 votes. For A: Output going to stdout?
Scholar 6 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Scholar 6 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
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
Scholar 7 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
Scholar 9 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 10 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
Scholar 10 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: 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)?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 15 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Guru 15 months ago, received more than 100 upvotes.

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