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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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--update does only update Pangolin or Nextclade ? #181

Closed hoelzer closed 2 years ago

hoelzer commented 2 years ago

I'am not 100% sure about this but I started the pipeline today and the new pangolin container was pulled and used

nanozoo/pangolin:3.1.17--2021-11-25

However, I then ended up with the pipeline using an older Nextclade container. I resumed the pipeline and now also the newest Nextclade container was pulled

nanozoo/nextclade:1.7.0--2021-12-09

Due to how the update feature is implemented, can it be that in case both containers are updated that only one is pulled? Or was this just some typical edge case of mine? ;)

replikation commented 2 years ago

mh not really, it should execute both updates together

its

  1. check if dockerhub can be reached using exemplary the pangolin dockerhub page, this
  2. if it can be reached extract the latest release name for nextclade and pangolin, this

these "latest names" are then printed to the terminal also

replikation commented 2 years ago

iam extracting from this page (https://registry.hub.docker.com/v2/repositories/nanozoo/nextclade/tags/) and the latest build docker container is the first one as its sorted by this date structure: "2021-12-12T01:24:15.740459Z"

hoelzer commented 2 years ago

Alright, yeah should work then. It might be also rare that we have updates of both containers - except when someone did not run and update the pipeline for a while (or a new VOC appears). We can also close this for now and just keep it in mind - let's see if this pops up again.