Bump GUNC and add gunc/run test #6920
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@dialvarezs this looks good but the module updates need to come via PRs into https://github.com/nf-core/modules and added to the pipline with |
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@jfy133 I don't get what you mean exactly. This is nf-core/modules, or am I doing something wrong? |
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I mixed up my PRs, sorry @dialvarezs ! You're all good here once snapshots updated 😅 (thoguht this was the mag PR...) |
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I guess these tests are too much for GitHub runners 🤔 |
| process { | ||
| withName: CHECKM_QA { | ||
| ext.args = "--tab_table" | ||
| } | ||
| } |
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There is nicer method of specifying these now with instructions merged in last week, so they are next to the test definition, try it out!
https://nf-co.re/docs/guidelines/components/modules#configuration-of-extargs-in-tests
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I tried it but setting the params inside run() doesn't seem to work (and it's not covered in the docs), so I left the args in nextflow.config again.
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@jfy133 Would it be possible to merge this despite the failing tests? The failures are because GitHub runners are running out of space while uncompressing the database, which seems unavoidable. |
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Mmm it's not ideal... How big is the database? |
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Around 21G (7 compressed + 14 uncompressed) |
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well poop. I guess course of action:
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* Bump GUNC and add gunc/run test * Fix meta, use input_dir * Add snapshots * Change strategy to preserve filenames * Add gunc/mergecheckm test * Update tags * Fix test names * Update snapshots * Add stubs * Add stub snaps * Address review comments * Set args in nextflow.config again * Comment problematic tests * Comment another test --------- Co-authored-by: Edmund Miller <[email protected]>
This PR includes:
PR checklist
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