User: kaushik.ghose
kaushik.ghose • 70
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Posts by kaushik.ghose
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... 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.ghose • 70
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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.ghose • 70
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... 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.ghose • 70
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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.ghose • 70
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... 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.ghose • 70
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... Could you try "*.tsv" for the glob please? ...
written 23 months ago by
kaushik.ghose • 70
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... 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.ghose • 70
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... 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.ghose • 70
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... 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.ghose • 70
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... 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.ghose • 70
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