User: anton.khodak

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Posts by anton.khodak

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Answer: A: CWL: reading filenames from another file in the runtime and treating them as fil
... Changing "path" to "location" and adding "file://" at the beginning of the file path in the last Javascript expression did the trick for (var j=0; j < line.length; j++){ if (line[j].startsWith('/')){ line[j] = { ...
written 3.4 years ago by anton.khodak0
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Comment: C: CWL: reading filenames from another file in the runtime and treating them as fil
... Could you please elaborate on the workaround? I don't quite understand what else an ExpressionTool can do here. Can I declare inputs and not provide them in the job, but populate them in the runtime? ...
written 3.4 years ago by anton.khodak0
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CWL: reading filenames from another file in the runtime and treating them as files
... I have the following set: One input parameter is a tab-delimited file with names of other files which will be used later. { "inputSamplesFile": { "class": "File", "path": "/path/to/inputSamples.txt" } ... other input parameters } inputSamples.txt NA12 ...
common-workflow-language cwl written 3.4 years ago by anton.khodak0
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Comment: C: CWL: reading files within an expressionTool
... Great example, thank you a lot! Just one question: why are `filename` and `filecontents` returned in the body of `processedoutput`, though you did not push them into this object explicitly? ...
written 3.4 years ago by anton.khodak0
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Comment: C: How to specify an optional input for a complex type in CWL?
... Could you please point to the second approach in the docs? As far as I remember, I found that on GitHub, not in the documentation. ...
written 4.1 years ago by anton.khodak0
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Comment: C: How to specify an optional input for a complex type in CWL?
... I'm sorry, I checked the job file and found out that I confused an underscore with a dash in the argument name... ...
written 4.1 years ago by anton.khodak0
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How to specify an optional input for a complex type in CWL?
... I need to pass an array as an optional argument in a CWL tool definition. I know that for primitive types `['null', ]` works fine, but for array it generates an error: `Type property "['null', 'array']" not a valid Avro schema`. I have also tried to specify it the next way: - id: bam_files ...
common-workflow-language cwl written 4.1 years ago by anton.khodak0 • updated 3.9 years ago by Michael R. Crusoe1.8k

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Scholar 3.4 years ago, created an answer that has been accepted. For A: CWL: reading filenames from another file in the runtime and treating them as fil

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