Pangolin4 update

[RaverJay]

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 https://github.com/replikation/poreCov/issues/226 )

[hoelzer]

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

[replikation]

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

additionally which columns do we need to track? @RaverJay

[replikation]

@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]

nanozoo/pangolin-v4:4.0--1.2.133

[RaverJay]

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]

Works now

[hoelzer]

awesome

[hoelzer]

"variants tableof" is missing a whitespace : )

[RaverJay]

"variants tableof" is missing a whitespace : )

fixed :D

[RaverJay]

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

[replikation]

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

[replikation]

• merging into release branch