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+ Input: Command line to run tool.
+ Distinguish from command line (parsing):
+ script
+ file
+ positional
+ flag
+ argument
+ Implement explicit markup of cli tokens to support funny scrip…
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The file could be read without storing it I think. I assume that you will receive 1 workflow in CWL and you can verify and parse it without storing it locally, something similar to:
`…
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This appears to be a typo that occurred from CWL to WDL transition, or perhaps existed since the creation of the non-human detect variants pipeline:
Relevant lines in detect_variants_nonhuman.wdl
…
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I've looked at the implementation of the [example of dirac production](https://gitlab.cta-observatory.org/cta-computing/dpps/workload/cwl_dev/-/blob/main/testProdDefinitions.py) into [CWL](https://git…
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Implement "proper" workflows by adding CWL support, which would parse the CWL and resolve it down in to the existing way of adding commands with dependencies.
Possibly useful:
https://github.com/r…
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We have gotten this requirement often.
https://cwl.discourse.group/t/dynamic-changing-docker-pull-registry-location-in-dockerrequirements/530
https://cwl.discourse.group/t/using-javascript-in-requ…
mr-c updated
2 months ago
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Using Docker images pulled from ECR would enable higher scalability when executing workload. We want to demonstrate how this is possible using a simple CWL workflow.
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Capture workflow run crate provenance from Snakemake workflows similar to existing CWL. Note that WfExS already is doing something similar (but to figure out workflow structure)
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One common CWL modality is to treat workflows as fairly opaque objects, converting carefully named workflow level inputs into the forms and names needed by the underlying tools. CWL 1.0 makes this fai…
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When using `toil-cwl-runner` it seems like it always uses `deep_listing` when files or directories are mounted for running within Docker or Singularity.
If I try to add [LoadListingRequirement](https…