Updates for pangolin v.4.0

[talnor]

What needs to be done:

Quite a lot of changes were made in pangolin version 4.0. Some of these changes are not compatible with gms-artic as is. The latest docker containers are therefore not working right now.

To pull a container with an older version of pangolin, run: docker pull genomicmedicinesweden/gms-artic-illumina:2022-04-01-p-3.1.20-L-2022-02-28-c-0.1.4-d-1.2.139-s-0.3.16

Important updates include (see the pangolin release and webpage for more info):

• The default mode is shifting from pangoLEARN to UShER. If you run large amounts of sequences through pangolin routinely you should be aware this update will impact the speed of pangolin
• pangoLEARN and pango-designation dependencies are replaced by pangolin-data
• The output csv file has changed slightly.

Suggestions on how to get it done:

• update environment.yml for nanopore and illumina
• update versions process in analysis.nf
• need for updating parsing of pangolin output?

What are the arguments for getting it done:

Task is considered finished when:

• [x] The tests have passed.
• [x] Update the workflows/build_dockerfile.yml so that they are updated automatically.

[talnor]

FoHM also wants these new output files named as 'pangolin_classification_format4.txt'

[henningonsbring]

FoHM also wants these new output files named as 'pangolin_classification_format4.txt'

I have made a PR to CG repo to deal with this

[sofstam]

I think we can close this issue.