Matthias Hörtenhuber

file entitites overwritten without warnig

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Hi, I am currently working on adding RO-crates to the nf-core CLI tools: https://github.com/nf-core/tools/pull/2680 nf-core pipelines usually have a root `main.nf` file, which should be a `ComputationalWorkflow` entity, but they...

Add new command nf-core rocrate to create a Research Object (RO) crate for a pipeline (continuation from #2680) [skip changelog]

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#2680 was auto-merged too fast. Continuing the work with this PR

### Description of the bug E.g. it throws a warning that it couldn't fine the multiqc config, even though it is due to it being skipped in the template render...

allow mixed str and dict in lint config

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we should probably rewrite this into a TypedDict or similar in the future.

Allow `main` as default channel

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Closes [#1931](https://github.com/nf-core/tools/issues/1931) ```[tasklist] - [x] switch tools repo to `main` - [ ] switch modules repo to `main` (build in logic to check default branch early, make switch later) -...

### Description of feature see https://github.com/nf-core/modules/blob/master/modules/nf-core/checkqc/main.nf for a module where this is not the case. Similar cases can be found with many python modules

> Kinda a seperate issue but thought it might be a good place for the discussion. > > > > I was thinking about this in terms of nf-core/modules. >...