Reference panel accepts a csv

[eugeniafontecha]

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/phaseimpute branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
• 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).

This PR addresses this issue #11

[LouisLeNezet]

Sorry @eugeniafontecha this code is a duplicate of #18
For it to works we need to correctly manage the files by chromosome and use the meta map accordingly.
You effectively saw the different problem I've ran into.
Could you look at my PR ? it contains all the modification you've done.

[atrigila]

Hi @LouisLeNezet!

I understand your concerns regarding the duplication of code but I would like to provide additional context. The contribution from @eugeniafontecha, while overlapping with your work, represents a unique effort during the hackathon that I believe deserves consideration.

This is one of Eugenia's first contributions in Nextflow and she went above and beyond during her first hackathon. I think it would be nice, as members of the nf-core community, to welcome participation from less experienced contributors.

Since Eugenia's code contains partially the same modifications as yours, you could perhaps review Eugenia's PR and consider how her modifications can complement and improve upon your work. Then, if you accept her PR, you can sync your code with these changes and then submit your additional modifications accordingly. I think that this way we all benefit and foster a supportive community :)

[LouisLeNezet]

@atrigila I understand completely.
It will break a few things on my PR but I will manage.
Would it be possible for her to do the following command ?

nf-core subworkflows update vcf_impute_glimpse
nf-core subworkflows update vcf_phase_shapeit5

[LouisLeNezet]

Nicely done ! Congrats on your first PR on this pipeline.
Looking forward to your next contributions. 😄

[LouisLeNezet]

We will merge even if the test fail as the #18 will fix it :)

[eugeniafontecha]

Thank you @LouisLeNezet and @atrigila !!