🧹 D3b-ify Sentieon Updates #15
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dmiller15
added
feature
| $include: ../scripts/get_dnascope_model.py | ||
| arguments: | ||
| - position: 0 | ||
| valueFrom: 'pip install pyyaml requests;' |
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Not sure I am a big fan of having to install a package every time. Can we find/create an image that has what's needed?
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Normally I'd agree but:
- this isn't part of the workflow and would only be run in a one-off context
- there really isn't a good docker out there that has pyyaml and requests built in
| secondaryFiles: | ||
| - pattern: .fai | ||
| required: true | ||
| - pattern: ^.dict |
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Is it that the dict is not actually needed, or the tool will create it if it doesn't exist?
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Hard to say. The tool is a bit of a panacea so it might be required for different run modes but not for everything.
| prefix: --minimap2_args | ||
| util_sort_args: | ||
| type: string? | ||
| doc: "Extra arguments for sentieon util sort (default: '--cram_write_options version=3.0,compressor=rans')" |
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So --util_sort_args takes in by default an arg that looks like an option? Maybe it's a wrapper thing that's not apparent from here
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That's what it says. Seems like it's the equivalent of doing "extra args"
| - pattern: .crai | ||
| required: false | ||
| outputBinding: | ||
| glob: ["*.cram", "*.bam"] |
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| glob: ["*.cram", "*.bam"] | |
| glob: "*.[b|cr]am" |
this works too, right?
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No. Haodong is leveraging the fact that CWL's glob declaration can take an array of strings. What you're probably thinking about is *.{b,cr}am which would be a singular string that can grab both BAMs and CRAMs. Both solutions are acceptable.
Co-authored-by: Miguel Brown <[email protected]>
Description
Ports over the changes made by Sentieon to their Long Reads workflows.
Integrates their new CLI tool and models
Type of change
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
Test Configuration:
Checklist: