Replace pool read includes with cat fastq modules for improved handling of single and paired reads

[Brijeshthummar02]

Closes #810

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---

Hi @Brijeshthummar02,

It looks like this pull-request is has been made against the Brijeshthummar02/mag main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the Brijeshthummar02/mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[jfy133]

I think this case I would just like to replace the module name where it's invoked (rather than using an alias)

Also you can remove the old local modules too if we are no longer using them :)

[Brijeshthummar02]

I think this case I would just like to replace the module name where it's invoked (rather than using an alias)

Also you can remove the old local modules too if we are no longer using them :)

Fixed

[jfy133]

Sorry @Brijeshthummar02 , by invoked I mean where the module is also used. I realise my suggestions weren't clear

So you need to do the following:

1. Have two include lines, with aliases of CAT_FASTQ_SHORT and CAT_FASTQ_LONG (before I meant don't retain the old name) around line 51 of mag.nf
2. Then replace the contents of the else between 356-363, and 364 with simply CAT_FASTQ_SHORT (don't need to use the old filters nor the mix), and possibly update the branch name used for assigning ch_short_reads_spades cahnnel
3. Replace lines 372-373 with CAT_FASTQ_LONG` accordingly
4. Delete the two modules/local/pool_* module filess

[Brijeshthummar02]

@jfy133 all code is missing after cfc76dc
PR is empty now.

[jfy133]

@jfy133 all code is missing after cfc76dc
PR is empty now.

Oops sorry @Brijeshthummar02 I forgot to say that the pool reads modules have moved from the main workflow to the short read preprocessing subworkflow!

Really sorry about that, you started just before a big bunch of refactoring - that's my fault for not warning you (I'm spinning too many plates at the moment)

[Brijeshthummar02]

Should i reopen the PR.?

[dialvarezs]

Hi @Brijeshthummar02. The code has been reorganized, but the issue is still not resolved. You can continue working on this PR using the current dev branch. Look for POOL_* module usages in the subworkflows, not in mag.nf.

[jfy133]

@dialvarezs maybe you can take over this one?