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Automate mitochondrial gene retrieval for SCTK QC - #904

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tilschaef wants to merge 10 commits into
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sctk-mt
Open

Automate mitochondrial gene retrieval for SCTK QC#904
tilschaef wants to merge 10 commits into
developfrom
sctk-mt

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@tilschaef

@tilschaef tilschaef commented Oct 14, 2022

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What problem is the PR solving / What's new?
Very hacky automated mitochondrial gene retrieval with genomepy for SCTK quality control (#847).

What did change

  • Use genomepy for mitochondrial gene list retrieval instead of sctk build in lists (limited species and provider)
  • Simplified config and schema

Checklist

  • I made a PR to develop (not master)
  • If applicable: I updated the docs
  • I updated the CHANGELOG
  • These changes are covered by the tests

@tilschaef tilschaef added the code design Code works, but needs improvement label Oct 14, 2022
@Maarten-vd-Sande

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@Rebecza is (potentially) going to finish PR 😄

@siebrenf siebrenf left a comment

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ah ok, I though you were wrapping up and requested a new review

@Rebecza

Rebecza commented Nov 17, 2022

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Good if we talk tmr morning some more about this in lab? 🤓

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4 participants