pangolin stub, nf-test, snap

[sateeshperi]

[sateeshperi]

not sure whats up with conda...have to check the bioconda recipe

[SPPearce]

csv output from docker:

taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note
"MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome",B.1,0.0,,,,,,PANGO-v1.17,4.2,0.3.17,v0.1.10,True,pass,Ambiguous_content:0.02,Assigned from designation hash.

csv output from conda:

taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note
"MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome",B.1,0.0,,,,,,PANGO-v1.28,4.2,0.3.19,v0.1.12,True,pass,Ambiguous_content:0.02,Assigned from designation hash.

This suggests there is a different database being used. Maybe seqera containers will fix this?

[sateeshperi]

closing in favor of #6740