User: kaushik.ghose

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Posts by kaushik.ghose

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Answer: A: Can I use output eval with CWL to create the list of output files (i.e. replace
... Hi! I suspect that the best way to do this is to have a small bash script that runs after the main script, reads `summary.txt` and copies those files to a new directory say `outputs` and the CWL declares the output to be that directory. The bash script can be either part of the docker image or injec ...
written 8 months ago by kaushik.ghose70
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Answer: A: bedtools sort -faidx in CWL
... Hello @dami, there was a typo in your `valueFrom` field the `{}` should not be there #!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool label: "sort a bed file based on occurrence in fasta" requirements: - class: DockerRequirement dockerPul ...
written 8 months ago by kaushik.ghose70
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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 14 months ago by kaushik.ghose70
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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 14 months ago by kaushik.ghose70
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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 23 months ago by kaushik.ghose70
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Comment: C: CWL: Getting output file of a CommandLineTool using glob
... Could you try "*.tsv" for the glob please? ...
written 23 months ago by kaushik.ghose70
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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 23 months ago by kaushik.ghose70
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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 2.2 years ago by kaushik.ghose70
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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 2.2 years ago by kaushik.ghose70
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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 2.2 years ago by kaushik.ghose70

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