New kma module #7251
New kma module #7251
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modules/nf-core/kma/kma/main.nf
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| tuple val(meta), path("*.res"), optional: true, emit: res | ||
| tuple val(meta), path("*.fsa"), optional: true, emit: fsa | ||
| tuple val(meta), path("*.aln"), optional: true, emit: aln | ||
| tuple val(meta), path("*.frag.gz"), optional: true, emit: frag | ||
| tuple val(meta), path("*.mat.gz"), optional: true, emit: mat // if mat_format == true | ||
| tuple val(meta), path("*.spa"), optional: true, emit: spa // if ext.args contains '-Sparse' (only output in this case) |
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why are all of them marked as optional?
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This is because of the tool's -Sparse option. {aln, res, frag, fsa} are returned in default mode. If the -Sparse option is used then only {spa} is returned. {mat} is in any of the former cases another optional output.
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ok then we can leave it like that :) but the stub needs to reflect that then (there you can check what is handed to the module and only create the file that you would expect)
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it seems you follow the Harshil Alignment style. If yes, you should align the commas not the word optional: Comma Example
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Can you update this to adhere to https://nf-co.re/docs/guidelines/components/modules#configuration-of-extargs-in-tests :)
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This is super helpful! Thanks for the pointer! 👍
Thanks for reviewing! nf-test is still WIP. In fact, I need my KMA_INDEX module merged to nf-core first in order to test the KMA_KMA module because I'd like to avoid pushing tool-specific testdata to nf-core. I am aiming for a nf-test similar to |
modules/nf-core/kma/kma/main.nf
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| tuple val(meta), path("*.res"), optional: true, emit: res | ||
| tuple val(meta), path("*.fsa"), optional: true, emit: fsa | ||
| tuple val(meta), path("*.aln"), optional: true, emit: aln | ||
| tuple val(meta), path("*.frag.gz"), optional: true, emit: frag | ||
| tuple val(meta), path("*.mat.gz"), optional: true, emit: mat // if mat_format == true | ||
| tuple val(meta), path("*.spa"), optional: true, emit: spa // if ext.args contains '-Sparse' (only output in this case) |
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it seems you follow the Harshil Alignment style. If yes, you should align the commas not the word optional: Comma Example
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Thanks @mazzalab , good catch about the Harshil Alignment style. Even though it hurts my eyes 😉 I'll adhere to the style with the next fix. |
PR checklist
Closes PR #7242
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda