Skip RUNDIRPARSER if no rundir information is available

[matrulda]

Fixes #166. The RUNDIRPARSER module is now skipped if there is no rundir information.

With this in place, I see no need to further document the rundir. It currently says it is optional and now it can be left empty without the pipeline breaking.

We probably should add a test for this (basically have a sample sheet with no rundir information), I have not done this (yet).

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/seqinspector 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).

[matrulda]

nf-core/test-datasets#1836 Needs to be merged before I can add a nf-test.

[matrulda]

@beatrizsavinhas Since you reported the issue it would be nice to have your input as well. Is the automatic skip enough or do we need more information about the run directory? 🙂

[beatrizsavinhas]

I think this is great! 🌟
In terms of usability I think this is good enough, but maybe it would be useful to have some written information somewhere about this step? Just so the user could know what it does and when it runs or not.
Perhaps something in the docs/usage.md file, in the table that lists the columns of the samplesheet, like this?

rundir	Path to the runfolder containing extra information about the sequencing run (optional*).

(...)

*If rundir is not provided, the RUNDIRPARSER module is skipped and the run metadata is not collected.

[matrulda]

I think this is great! 🌟 In terms of usability I think this is good enough, but maybe it would be useful to have some written information somewhere about this step? Just so the user could know what it does and when it runs or not. Perhaps something in the docs/usage.md file, in the table that lists the columns of the samplesheet, like this?

rundir
Path to the runfolder containing extra information about the sequencing run (optional*).

(...)
*If rundir is not provided, the RUNDIRPARSER module is skipped and the run metadata is not collected.

Sounds great, will fix! Thank you! 🙏

[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.

[matrulda]

@maxulysse Is this Ok to merge now? I'm thinking the template update could be taken care of in another PR?