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Adding a filtering step to handle unplaced chromosomal sequences. V2 #114
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This PR is against the
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looks ok to me, just need to be sure that it's working, if I remember well, that was our whole issue there |
@Shaun-Regenbaum sorry about that, but I'd reckon we'd need to fix the conflicts |
Im going to try update this and get it working |
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. |
@Shaun-Regenbaum sorry for introducing a lot of merge conflicts, I'll open up a new PR with your changes applied on the current |
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?
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Closing this as #177 implements these changes on the latest |
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.