Add gtf2featureannotation module

[pinin4fjords]

PR checklist

Adding module wrapper for https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. See also https://nfcore.slack.com/archives/CJRH30T6V/p1665413183508719.

Apologies for the long name, didn't quite think that through at the time I wrote this tool!

Closes https://github.com/nf-core/modules/issues/2316

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• [x] If you've fixed a bug or added code that should be tested, add tests!
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• [x] If necessary, include test data in your PR.
• [x] Remove all TODO statements.
• [x] Emit the versions.yml file.
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• [x] Follow the parameters requirements.
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• [x] Add a resource label
• [x] Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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  • [x] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
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[pinin4fjords]

@nf-core-bot fix linting

[pinin4fjords]

Thanks for review @ramprasadn! Requested changes done.

[pinin4fjords]

Thanks for the guidance @ramprasadn - how's this?

[ramprasadn]

Module looks good, just a few changes to the docs and it should be 👌🏻

[pinin4fjords]

Module looks good, just a few changes to the docs and it should be 👌🏻

Done!

[ggabernet]

As I understand it, this module is for converting a GTF file to an annotation table. So within a pipeline, it will be called just once on the GTF file provided as reference. Actually in the case of operating on reference data the meta maps are not needed, as there is no sample-specific information to be forwarded to the module itself. See for example some genome indexing modules as the salmon index one (https://github.com/nf-core/modules/blob/master/modules/nf-core/salmon/index/main.nf).

[pinin4fjords]

As I understand it, this module is for converting a GTF file to an annotation table. So within a pipeline, it will be called just once on the GTF file provided as reference. Actually in the case of operating on reference data the meta maps are not needed, as there is no sample-specific information to be forwarded to the module itself. See for example some genome indexing modules as the salmon index one (https://github.com/nf-core/modules/blob/master/modules/nf-core/salmon/index/main.nf).

Haha- well, that was my original thinking, but you and @ramprasadn will have to fight it out :-D

The module has a lot of options for deriving the data in different ways, e.g. for different feature sets (e.g. genes, transcripts), so I can see the potential for multiple uses per workflow.

[ggabernet]

ok well if you can see the use to the meta map in the module, then it can always be provided as an empty list to the channel if not needed 👍

[pinin4fjords]

Thanks for reviews @ggabernet @ramprasadn !