Fix MultiQC file naming and publication

[JoseEspinosa]

Fix multiqc reports publication and centralize the config in modules.config:

• Rename pLDDT TSV output files from *_plddt.tsv to *_plddt_mqc.tsv so multiqc picks them up automatically.
• Centralize multiqc publish dir configuration in modules.config removing the duplicated per-model MULTIQC publish dir logic.

PR checklist

• This comment contains a description of changes (with reason).
• 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>).
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Closes #600

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Hi @JoseEspinosa,

It looks like this pull-request is has been made against the JoseEspinosa/nf-core-proteinfold master branch.
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Because of this, PRs to master are only allowed if they come from the JoseEspinosa/nf-core-proteinfold dev branch.

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Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[keiran-rowell-unsw]

Fix multiqc reports publication and centralize the config in modules.config:

* Rename pLDDT TSV output files from `*_plddt.tsv` to `*_plddt_mqc.tsv` so multiqc picks them up automatically.

Nice! For a future metrics release, just expanding here that I've added a proteinfold-specific multiqc config file so that various metrics can be picked up an handled appropriately in a MultiQC bulk report.

Does multiqc philosophy stipulate there must be still be canonical _mqc extensions, or is it okay once you've got a custom module?

[JoseEspinosa]

It is OK if they don´t have a _mqc, it it just the opposite if there is no custom multiqc config file the files are not picked up, so what it was happening is that the multiqc report in 2.0.0 was not including any plots. We could discuss if adding _mqc to multiqc files could be nice to identify them easily in your new implementation but if this files are going to be used elsewhere then maybe no 🤔

[JoseEspinosa]

If will be great if you could take a look left an approval (or your suggestions) @keiran-rowell-unsw so that we can merge it until the new procedure comes in. Thanks!

[keiran-rowell-unsw]

Looks fine to me!

I like the move to ${meta.model} in the ext.prefix.& the small nf.test suite changes.

[keiran-rowell-unsw]

If will be great if you could take a look left an approval (or your suggestions) @keiran-rowell-unsw so that we can merge it until the new procedure comes in. Thanks!

Done thanks! Yes I agree, sorry this broke in v2. The custom MultiQC & reporting can be done 'at once' in a major release.

With the _mqc extension, I was hoping to re-use the files in other places, so I'd rather MultiQC just use suffix by metric.
I had a chat with Gerardo Tauriello @ U. Basel yesterday on the metrics. They're keen to see how an implementation works in Nextflow, and everything we generate should map okay to their classes. ipSAE (#592) isn't well supported, but its the one metric they may add in the future.

[JoseEspinosa]

had a chat with Gerardo Tauriello @ U. Basel yesterday on the metrics. They're keen to see how an implementation works in Nextflow, and everything we generate should map okay to their classes. ipSAE (#592) isn't well supported, but its the one metric they may add in the future.

That sounds very interesting, if ipSAE is not fully supported yet, but if it is a metric they may add in the future, it probably makes sense to keep the implementation flexible enough to accommodate it later.