Adding a filtering step to handle unplaced chromosomal sequences. V2

[Shaun-Regenbaum]

This change fixes #112 among some other issues I saw people talking about in the slack for the past year or two.
Primarily it handles cases where before the exome.bed and genome.dict file had mismatches.

This should make the pipeline more resilient especially while using less common reference genomes (such as cow).

I ran the tests and they passed, not sure if we would want to include this in the changelog as its pretty minor.

Other that that, this is my first contribution to nf-core so would love feedback. Sorry about the repeat PR #113 , I just pulled the wrong version.

[github-actions]

This PR is against the master 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

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Hi @Shaun-Regenbaum,

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

[maxulysse]

looks ok to me, just need to be sure that it's working, if I remember well, that was our whole issue there

[maxulysse]

@Shaun-Regenbaum sorry about that, but I'd reckon we'd need to fix the conflicts

[Shaun-Regenbaum]

Im going to try update this and get it working

[Shaun-Regenbaum]

I actually odon;t know about this yet, everything is kind of a mess and doesn't work properly with nf-core tools right now, so I don't even know where there are conflicts, I am going to abandon this again for now.

[nvnieuwk]

@Shaun-Regenbaum sorry for introducing a lot of merge conflicts, I'll open up a new PR with your changes applied on the current dev code. Is it okay if I ask for your review on that one?

[Shaun-Regenbaum]

Sure! No problem :)

…

On Thu, Feb 27, 2025 at 4:30 PM Nicolas Vannieuwkerke < ***@***.***> wrote: @Shaun-Regenbaum <https://github.com/Shaun-Regenbaum> sorry for introducing a lot of merge conflicts, I'll open up a new PR with your changes applied on the current dev code. Is it okay if I ask for your review on that one? — Reply to this email directly, view it on GitHub <#114 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADANAZDLJ6BZPJWLRGYHFZD2R4VRRAVCNFSM6AAAAABYAD6HQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBYGMYDMOBSGE> . You are receiving this because you were mentioned.Message ID: ***@***.***> [image: nvnieuwk]*nvnieuwk* left a comment (nf-core/rnavar#114) <#114 (comment)> @Shaun-Regenbaum <https://github.com/Shaun-Regenbaum> sorry for introducing a lot of merge conflicts, I'll open up a new PR with your changes applied on the current dev code. Is it okay if I ask for your review on that one? — Reply to this email directly, view it on GitHub <#114 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADANAZDLJ6BZPJWLRGYHFZD2R4VRRAVCNFSM6AAAAABYAD6HQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBYGMYDMOBSGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[nvnieuwk]

Closing this as #177 implements these changes on the latest dev branch