Nextclade docker update

[replikation]

• included now nextclade for --update

• nextclade containers are build every week

• they contain nextclade version and the date of the data (like pangolin)

• this information is also noted in the final report (version + data)

• @hoelzer can you please test this build via singularity using the --update flag ?

[replikation]

• set the default basecaller and medaka model to "hac". Using "sup" is up to the user

[hoelzer]

@replikation looks basically good and runs also in our restricted environment w/ Singularity. But I noticed some difference regarding deletions in Delta sequences. Basically, w/ v0.10.3 we always see the deletion

S:F157-, S:R158-

but with the current nextclade_docker_update branch we always see

S:E156-, S:F157-

So shifted by one position. The other SNPs seem fine. Another Delta-characteristic deletion at position

ORF8:D119-, ORF8:F120-

ist not touched... so stays same between the two versions.

Any idea where this difference could come from? 0_0

v0.10.3

This branch

[hoelzer]

One second... you extract the information about insertions and deletions from the Nextclade output, right? Then there might be a difference between the quite old and new nextclade version and that causes the difference. Actually, the new positions might be even more accurate

[hoelzer]

yep, the consensus sequences are exactly the same (same md5sum) but Nextclade versions annotate this specific deletion position differently. Hach, Friday edge case discovered :leichtes_lächeln: but that's fine I would say. Likely even more accurate then the old Nextclade information

[replikation]

ah yes nexclade is new they adjusted some things. the nextclade version and database version is now also noted on the final report to avoid "differences" between databases. Thank you ill do some testing merge and prep a release