Added parallel version of ltrharvest #4968
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modules/nf-core/ltrharvest/meta.yml
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| tools: | ||
| - "edta": | ||
| description: Extensive de-novo TE Annotator (EDTA) | ||
| homepage: "https://github.com/oushujun/EDTA" | ||
| documentation: "https://github.com/oushujun/EDTA" | ||
| tool_dev_url: "https://github.com/oushujun/EDTA" | ||
| doi: "10.1186/s13059-019-1905-y" | ||
| licence: ["GPL v3"] | ||
| - "gt": | ||
| description: "The GenomeTools genome analysis system" | ||
| homepage: "https://genometools.org/index.html" | ||
| documentation: "https://genometools.org/documentation.html" | ||
| tool_dev_url: "https://github.com/genometools/genometools" | ||
| doi: "10.1109/TCBB.2013.68" | ||
| licence: ["ISC"] |
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This is unusual, but I guess it makes sense.
Include an entry specifically for 'ltrharvest' so it's origin is clear
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Thank you @mahesh-panchal
I have added an entry for LTR_harvest_parallel.
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() }, | ||
| { assert snapshot(path(process.out.versions[0]).text).match("stub_versions") } |
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the stub_versions and script_versions snapshots look the same. I think you can share those snapshots between test cases (.match("versions")) since the script and stub blocks use the exact same logic
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it would also be ok to remove this check entirely or loosen it a bit to just check for existence, so you don't need to update the snapshots for minor version bumps... but its fine if you want to be conservative here
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Hi @ahvigil
Thank you for the feedback. It is not possible anymore to use the same snapshot name. nf-test doesn't allow that anymore.
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ugh thats too bad but it seems you're right: askimed/nf-test#188
however, there is an open issue to provide an opt in for cases like this where it might be useful to remove repetition: askimed/nf-test#197. Hope they can implement something like that!
* Added parallel version of ltrharvest * Removed scn from snapshot * Added entry for LTR_HARVEST_parallel in meta.yml
* Added parallel version of ltrharvest * Removed scn from snapshot * Added entry for LTR_HARVEST_parallel in meta.yml
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda