Closed replikation closed 3 years ago
replikation
commented
3 years ago replikation
commented
3 years ago -c pangolin.config
hoelzer
commented
3 years ago * @hoelzer you can also always provide the latest pangolin version / container via `-c pangolin.config`
ah okay, this would be then a way to not touch poreCov all the time.
a) (auto)build the new container on Dockerhub
b) adjust the pangolin.config for config injection in the poreCov run
But then I also have to maintain a pangolin.config file - then i can also maintain the poreCov config ;)
hoelzer
commented
3 years ago uh @replikation maybe we can just do a
pangolin --updateinside of the pangolin process? Afaik it will then check for the newest pangoLEARN version... but not sure if this will work inside of a Docker/Singularity container...
replikation
commented
3 years ago @hoelzer would do an update for each fasta file. could be done but still we need to get then the version
find a way in nextflow to implement always the latest pangolin version in poreCov but report back pangolin and pangoleran version.
setup "weekly" or every x day pangolin docker images.
Solutions: 1) not sure if I can "URL-fetch" in groovy the latest container and put this in as a variable?
if not found use "latest" local available variant? 2) could use "latest" and "grep" version (similar to what nf-core is doing) - this way so auto build not just a version, build also a "latest" container. but would be good if the user can then specify the docker.
dockerimage tag for daily build:
nanozoo/pangolin:pangolinversion--pangolearnversion-- so its only pushed if "new"