Maxime U Garcia

fix(schema): fix typo (strelka2 -> strelka)

3

## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

### Description of the bug I think if we don't download cache there's still an empty folder created, so let's check that out ### Command used and terminal output _No...

port CREATE_INTERVALS_BED to nf-core/modules

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### Description of feature That would be actually necessary to port all our subworkflows with intervals to nf-core

Sanitize path

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### Description of the bug params.outdir + "/path/output/" -> file(params.outdir + "/path/output/").toUriString() ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System information _No response_

test it out

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## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

Split variantannotation in its own pipeline and import it

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## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

Hey, this problem has not been entirely fixed... I am running with a local genome with` ignore igenomes` set and have a sample sheet with both status entered: 0 and...

Not great having to disable more nf-tests :-/ _Originally posted by @asp8200 in https://github.com/nf-core/sarek/pull/1545#pullrequestreview-2104419382_

https://github.com/asp8200/sarek/blob/8d1592c242fbb2bd2cc7da66377032d55afc7816/workflows/sarek/main.nf#L270 https://github.com/asp8200/sarek/blob/8d1592c242fbb2bd2cc7da66377032d55afc7816/workflows/sarek/main.nf#L288 I just hope we have CI-tests covering all this intricate stuff 🤞 _Originally posted by @asp8200 in https://github.com/nf-core/sarek/pull/1541#discussion_r1615662778_

Adding stubs at all level

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- No stubs for `utils_*` subworkflows (local or from nf-core as no process so no stubs). - modules/local: - https://github.com/nf-core/rnaseq/pull/1331 - modules/nf-core: - https://github.com/nf-core/modules/pull/5854 - https://github.com/nf-core/modules/pull/5861 - subworkflows/local: - This...