User: kaushik.ghose

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Posts by kaushik.ghose

<prev • 9 results • page 1 of 1 • next >
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Answer: A: [cwl workflow steps] explicit I/O relationship, workflow
... As mentioned in that [issue][1]: > CWL is declarative in nature, so you can't directly control these steps (and should not have to, like in functional programming). > > The reason why you have an order of operations is because there is a dependency, perhaps hidden, in those steps. In CWL, ...
written 11 weeks ago by kaushik.ghose50
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Answer: A: cwl kubernetes support?
... Hi @xiao2, From the list of [CWL runners/implementations](https://www.commonwl.org/#Implementations) You could try [REANA][1]. Apache-Airflow supports Kubernetes, so perhaps [CWl-Airflow][2] would also work. [1]: https://reana.readthedocs.io/en/latest/index.html [2]: https://github.com/Bars ...
written 11 weeks ago by kaushik.ghose50
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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 12 months ago by kaushik.ghose50
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Comment: C: CWL: Getting output file of a CommandLineTool using glob
... Could you try "*.tsv" for the glob please? ...
written 12 months ago by kaushik.ghose50
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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 12 months ago by kaushik.ghose50
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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 15 months ago by kaushik.ghose50
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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 15 months ago by kaushik.ghose50
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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 15 months ago by kaushik.ghose50
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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 15 months ago by kaushik.ghose50

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