Issue #817: Restructure local module and subworkflows into dedicated directories

[Brijeshthummar02]

PR checklist

Fixes #817

• 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/mag 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).

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

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]

Hi @Brijeshthummar02 ! Thanks for picking this up :D

I will properly review in a bit (breakfast time), but first:

• Please join the nf-core github organisation by following instructions here: https://nf-co.re/join (that way I don't need to approve each CI run)
• Please don't forget to add a CHANGELOG entry and add yourself to the contributors list in the README :)

[jfy133]

@Brijeshthummar02 You need to check some of the subworkflows, as some of the modules you've renamed are loaded into the subworkflows

[Brijeshthummar02]

@Brijeshthummar02 You need to check some of the subworkflows, as some of the modules you've renamed are loaded into the subworkflows

Yeah sure, as i was in bit hurry so didn't see it. If possible can you mention here directly.

Also i have send the message on slack channel to add me to org.

[jfy133]

@Brijeshthummar02 you should have received the github invitation

[Brijeshthummar02]

Hi @Brijeshthummar02 ! Thanks for picking this up :D

I will properly review in a bit (breakfast time), but first:

• Please join the nf-core github organisation by following instructions here: https://nf-co.re/join (that way I don't need to approve each CI run)
• Please don't forget to add a CHANGELOG entry and add yourself to the contributors list in the README :)

Can you specify file path where to add my name i did not see any list in README.

[jfy133]

Can you specify file path where to add my name i did not see any list in README.

Root README.md:

mag/README.md

Lines 89 to 100 in 7ffd8b8

	- [Antonia Schuster](https://github.com/AntoniaSchuster)
	- [Alexander Ramos](https://github.com/alxndrdiaz)
	- [Carson Miller](https://github.com/CarsonJM)
	- [Daniel Lundin](https://github.com/erikrikarddaniel)
	- [Danielle Callan](https://github.com/d-callan)
	- [Gregory Sprenger](https://github.com/gregorysprenger)
	- [Jim Downie](https://github.com/prototaxites)
	- [Phil Palmer](https://github.com/PhilPalmer)
	- [@willros](https://github.com/willros)
	- [Adam Rosenbaum](https://github.com/muabnezor)
	- [Diego Alvarez](https://github.com/dialvarezs)
	- [Nikolaos Vergoulidis](https://github.com/IceGreb)

[jfy133]

@Brijeshthummar02 You need to check some of the subworkflows, as some of the modules you've renamed are loaded into the subworkflows

This still needs more addressed. If you run a few test runs it should tell you the issue.

Also if you use the Nextflow VSCode extension (assuming you use VScode) it should also tell you where you have include path problems

[Brijeshthummar02]

@Brijeshthummar02 You need to check some of the subworkflows, as some of the modules you've renamed are loaded into the subworkflows

This still needs more addressed. If you run a few test runs it should tell you the issue.

Also if you use the Nextflow VSCode extension (assuming you use VScode) it should also tell you where you have include path problems

Can you mention what kind of i should run for testing also as you see i tried to update path with correct name but still goes red

[jfy133]

@Brijeshthummar02 You need to check some of the subworkflows, as some of the modules you've renamed are loaded into the subworkflows

This still needs more addressed. If you run a few test runs it should tell you the issue.
Also if you use the Nextflow VSCode extension (assuming you use VScode) it should also tell you where you have include path problems

Can you mention what kind of i should run for testing also as you see i tried to update path with correct name but still goes red

e.g. nextflow run Brijesthummar02/mag -r main.nf -profile test,docker --outdir ./results

[jfy133]

You can also see in the CI test details

[jfy133]

Hi @Brijeshthummar02 do you think you will be able to continue this (and the other PR)?

[Brijeshthummar02]

I am trying to fix ci, but stuck don't know how to do so.

[jfy133]

The CI you can ignore for now :)

We are transitioning to nf-test so it will fail (hopefully working by end of today)

In the meantime you can run the commands locally for testing :)

[jfy133]

@Brijeshthummar02 if you merge in dev, the tests should pass now (assuming your code is working)

[Brijeshthummar02]

@Brijeshthummar02 if you merge in dev, the tests should pass now (assuming your code is working)

I will update you soon.

[dialvarezs]

Hi @Brijeshthummar02,
Would you be able to finish this PR and #818? We're preparing a new release, and it would be nice to include the changes from your PRs. If you're unable to complete them, no worries, but I’ll close them as stale.

[jfy133]

@dialvarezs maybe you can finish this one too :)