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Automate mitochondrial gene retrieval for SCTK QC #904

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Automate mitochondrial gene retrieval for SCTK QC #904

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tilschaef
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@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 reviewed Nov 16, 2022
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ah ok, I though you were wrapping up and requested a new review

@Rebecza
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Rebecza commented Nov 17, 2022

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

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@siebrenf siebrenf siebrenf approved these changes

@Maarten-vd-Sande Maarten-vd-Sande Awaiting requested review from Maarten-vd-Sande Maarten-vd-Sande is a code owner

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@tilschaef @Maarten-vd-Sande @Rebecza @siebrenf