Added 2FAST2Q module

[afombravo]

No description provided.

[SPPearce]

Is there a reason it isn't called 2fastq? Did something fall over because of the number at the start?

[afombravo]

The reason I am "filling" it as fast2q is because the PyPI module is called fast2q (numbers at the start are a no go naming wise). The same for nextflow processes I find out? So, despite the tool being published as 2FAST2Q, internally I am keeping it as fast2q, in line with nomenclature.

[SPPearce]

The reason the I am "filling" it as fast2q is because the PyPI module is called fast2q (numbers at the start are a no go naming wise), the same for nextflow processes i find out? So, despite the tool being published as 2FAST2Q, internaly I am keeping it as fast2q in line with numenclature.

Ok, that's fine, if it can't be 2FAST2Q then FAST2Q sounds like the best option.

[afombravo]

This is apparently failing on the tests. @SPPearce you are more experienced. Could you provide some insight to what I need to change, please? Cheers!

[afombravo]

@SPPearce The test errors I am getting now are due to some issue loading the right data. I am trying to use 2 files from here: https://github.com/nf-core/test-datasets/tree/crisprseq/testdata but the errors I am getting from the 2FAST2Q are related with the the files not being correct (either the wrong extention, or the wrong format). I know the files are right and the programs works with them "outside" nextflow, so, could it be some issue loading the right data from modules_testdata_base_path on nextflow.config?

[SPPearce]

You shouldn't be trying to set modules_testdata_base_path here, that is globally set.
Ideally, you'd copy any required data into the modules branch on the test-datasets repository.
Currently, I think you are pointing at a github webpage, you'd need to change it to the raw data link on github:
https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/crisprseq/testdata/SRR8983579.small.fastq.gz.
However, I would suggest that you just use some of the already existing data in the test-datasets repository; it doesn't necessarily have to be particularly meaningful the output.

[afombravo]

@SPPearce Do you think this is ready for clousure :) ?

[SPPearce]

@SPPearce Do you think this is ready for clousure :) ?

I made some changes (more than I could do easily via comments), see what you think.

[afombravo]

@SPPearce Do you think this is ready for clousure :) ?

I made some changes (more than I could do easily via comments), see what you think.

wow you really dug into it... I appreciate it! I will fix the linting and then resubmit!

[SPPearce]

@SPPearce Do you think this is ready for clousure :) ?

I made some changes (more than I could do easily via comments), see what you think.

wow you really dug into it... I appreciate it! I will fix the linting and then resubmit!

Sorry, I didn't notice you saying that you'd fix the linting; I've just done that.
You might want to update the descriptions in the meta.yml; I didn't know what the figures actually are.

[afombravo]

@SPPearce Do you think this is ready for clousure :) ?

I made some changes (more than I could do easily via comments), see what you think.

wow you really dug into it... I appreciate it! I will fix the linting and then resubmit!

Sorry, I didn't notice you saying that you'd fix the linting; I've just done that. You might want to update the descriptions in the meta.yml; I didn't know what the figures actually are.

No problem. I will do that then!

[afombravo]

@SPPearce Thank you so much! Your help was invaluable in this entire process.

[SPPearce]

Need to get someone else to review it that isn't me now, asking on the request-review channel on the nf-core slack is generally a good way

[kubranarci]

left small commends, otherwise LGTM!