Update modules

[FernandoDuarteF]

Closes #195.

Changes

• Updated all modules using nf-core modules update
• Removed appending versions channel outputs from modules with the new "topics" channel.
• Fixed linting (although it doesn't seem to work when running the CI checks). Might be worth ignoring these files.

Comments

Some nf-core modules don't have the topics channel to collect the versions. See these bellow. Might be worth migrating these first in the nf-core modules repo before merging this PR.

I will also change the local modules to incorporate the new "topics" channel.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/genomeqc branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[FernandoDuarteF]

Modules in nf-core/modules that have not been updated to topics channel yet:

• fastavalidator
• tidk/explore
• tidk/plot
• tidk/search

- repeatmasker/repeatmasker
- repeatmasker/builddatabase
- repeatmasker/repeatmodeler

I'm working on fcs/fcsadaptor. See nf-core/modules#10939. The repeatmasker modules are not part of this PR, so we can ignore them for now.

[FernandoDuarteF]

I think the EXTRACT_SEQS module can be removed.

[FernandoDuarteF]

Same container should be use for the shiny app and the tree plot. I'll make sure this is the case.

[FernandoDuarteF]

The tidk modules and subworkflows have been updated. Removed fastavalidator since tool is deprecated (might be worth looking for another alternative).

[FernandoDuarteF]

I think this is ready to merge.