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User: kaushik.ghose

gravatar for kaushik.ghose
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Posts by kaushik.ghose

<prev • 7 results • page 1 of 1 • next >
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Comment: C: CWL: Getting output file of a CommandLineTool using glob
... Are the files being produced in the working directory? Do you have Rabix Executor installed by any chance: (https://github.com/rabix/bunny). Might be worth trying on that too. ...
written 3 months ago by kaushik.ghose • 30
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Comment: C: CWL: Getting output file of a CommandLineTool using glob
... Could you try "*.tsv" for the glob please? ...
written 3 months ago by kaushik.ghose • 30
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Answer: A: CWL: Getting output file of a CommandLineTool using glob
... Hi! On the face of it the tool is not producing the abundance.tsv. When you run the tool bare (by yourself) do you see that .tsv file produced? ...
written 3 months ago by kaushik.ghose • 30
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Comment: C: CWL: Can we create a workflow model without the need for execution of the script
... Also found [cwlviewer][1], though I haven't used it yet [1]: https://github.com/common-workflow-language/cwlviewer ...
written 6 months ago by kaushik.ghose • 30
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Answer: A: CWL: Can we create a workflow model without the need for execution of the script
... Yes, this is completely possible. For example you can use the Rabix composer tool to map out the nodes and connections. This gives you a visual depiction of the workflow, which you can then export to json CWL representation. ...
written 6 months ago by kaushik.ghose • 30
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Comment: C: CWL: Is there a way to only pass certain fields from a `record` type to a step?
... Is this because you are sharing that record among many steps in a workflow, like [this use case][1]? [1]: https://www.biostars.org/p/306782/ ...
written 6 months ago by kaushik.ghose • 30
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Answer: A: More concise way to pass many parameters through to subworkflows
... One solution, not a very elegant one, would perhaps be to supply a text file (say a YAML file) with all the parameter (name, value) pairs, as a shared input to each tool. Each tool then has javascript in the CWL that grabs the parameters it requires (use load_contents to read the file contents into ...
written 6 months ago by kaushik.ghose • 30

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