Update output files to include nextclade information

[pbiology]

What needs to be done:
Look at the current output files and re-work the column order and names to match what Jan Albert have suggested recently.

Suggestions on how to get it done:

What are the arguments for getting it done:
More compatible with the needs to clinical microbiology

Task is considered finished when:

[pbiology]

Could you flesh this out a bit @karlnyr?

[sofstam]

I had started writing an issue, hope it is ok that I post this comment here.

After nextclade.csv is delivered to caesar, we talked about parsing of deliverables as a later step.

The current results.csv file looks as:

Sample,Selection,Region Code,Ticket,%N_bases,%10X_coverage,QC_pass,Lineage,Pangolin_data_version,VOC,Mutations
22CS999901,Information saknas,01,489423,2.31,99.17,TRUE,AY.45,PUSHER-v1.12,No,D614G;H655Y;P681R
22CS999902,Information saknas,01,489423,0.64,99.4,TRUE,AY.43,PUSHER-v1.12,No,D614G
22CS999903,Information saknas,01,489423,4.44,97.39,TRUE,AY.5,PUSHER-v1.12,No,D614G;P681R
22CS999904,Information saknas,01,489423,16.93,88.85,FALSE,AY.4,PUSHER-v1.12,No,L452R;T478K;D614G;P681R
22CS999905,Information saknas,01,489423,99.8,0.0,FALSE,Unassigned,PUSHER-v1.12,No,-
22CS999906,Information saknas,01,489423,2.41,98.03,TRUE,AY.43,PUSHER-v1.12,No,L452R;D614G

The column Lineage has to take information from Nextclade instead and the variants coming from Pangolin should be added as an extra column.

So, the file would look like:

Sample,Selection,Region Code,Ticket,%N_bases,%10X_coverage,QC_pass,Lineage,Pangolin_data_version,VOC,Mutations,Pangolin(or whatever name)

[sofstam]

The containers on stage are updated and they are having the latest nextclade version.

/home/proj/stage/mutant/MUTANT/mutant/externals/gms-artic

[talnor]

Asked KS about the updates. Got the following response:

I ett första steg så tycker jag att den vanliga resultat-filen inte ska uppdateras. Först behöver vi validera att den nextclade variant call vi får från CG stämmer med den vi får om kör fasta-filen på online nextclade.

Let's wait for go ahead on the deploy of these updates.