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]

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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.