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Pangolin4 update #224

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merged 11 commits into from
Apr 12, 2022
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RaverJay
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@RaverJay RaverJay commented Apr 1, 2022

closes #220

  • uses pangolin results for getting the versions for: pangolin version, pangolin-data version, scorpio version, constellation version (instead of complicated extra inputs)
  • report now appropriately writes pangolin-data instead of PangoLEARN

Cannot test for now, need the 4.0 container :)

Edit: Added nextclade private mutation information to the datatable ( closes #226 )

@hoelzer
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hoelzer commented Apr 1, 2022

wow, this was even faster then the new version can be on bioconda :D

@replikation
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replikation commented Apr 1, 2022

so what versions do we need to track now? pangolin version and pangolindata?

additionally which columns do we need to track? @RaverJay

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@RaverJay iam currently tracking the following columns for the autobuild to ensure that they are present for your report, this would be fine?

"taxon," || exit 1; }
 ",lineage," || exit 1; }
",conflict," || exit 1; }
",pangolin_version," || exit 1; }
 ",scorpio_version," || exit 1; }
 ",constellation_version," || exit 1; }
 ",qc_status," || exit 1; }
 ",qc_notes," || exit 1; }

if yes ill start the build and post the new docker name here. ill need to add a few other commits on top of it too (so that e.g. --update works fine)

@replikation replikation added the enhancement New feature or request label Apr 1, 2022
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nanozoo/pangolin-v4:4.0--1.2.133

@RaverJay
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RaverJay commented Apr 5, 2022

Pulling and testing now

The (new) report uses these columns:

taxon,lineage,conflict,scorpio_call,scorpio_conflict
version,pangolin_version,scorpio_version,constellation_version

@RaverJay
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RaverJay commented Apr 5, 2022

Works now

image

image

@hoelzer
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hoelzer commented Apr 5, 2022

awesome

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hoelzer commented Apr 5, 2022

"variants tableof" is missing a whitespace : )

@RaverJay
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RaverJay commented Apr 5, 2022

"variants tableof" is missing a whitespace : )

fixed :D

@RaverJay
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RaverJay commented Apr 5, 2022

Added nextclade private mutation information to the datatable ( closes #226 )
Somewhat unrelated, but a minor change

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@RaverJay added the columns to the docker autobuild to check if they are present

@replikation replikation changed the base branch from master to release1.5 April 12, 2022 07:36
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  • merging into release branch

@replikation replikation merged commit cc2d5b9 into replikation:release1.5 Apr 12, 2022
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Private mutation from nextclade Pangolin v4.0
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