pangolin v2.4.2

Release notes

• Update to minimap2 call to exclude secondary chains from output sam

minimap2 -a -x asm5 --sam-hit-only --secondary=no -t  {workflow.cores} {input.reference:q} '{input.fasta}'

• Bug fix from issue #184 where the case of all sequences failing quality control didn't match output of successful run.

pangolin v2.4.1

Release notes

• Update to output file format, now reporting pangolin version, pangoLEARN version and pango-designation version with assignments.

taxon,lineage,conflict,pangolin_version,pangoLEARN_version,pango_version,status,note
outgroup_A,A,0.0,2.4.1,2021-04-28,v1.1.23,passed_qc,

• Fixing bug in issue #181 that was introduced in previous release that caused duplicate names output if sequences failed to map.
• Fixing number reported for P.1 flagged in issue #180

pangolin v2.4

Release notes

Updates to pangolearn.smk:

• Now only map a single time producing a sam file, resulting in speed ups to pangolin
• gofasta now muiltithreading, additional speedups

Updates to output file:

• Output 'conflict' rather than 'probability' now, this is a measure of conflicts within the decision tree, 0 being equivalent to no conflicts, but not a confidence score.
• Output the pango-designation version number now, which is available from pangoLEARN version 2021-04-28 onwards.

Bug fixes:

• Noted discrepancies between minimap -a and minimap without the -a flag, leading to occasional sequences not accounted for in output csv file. This only occured when minimap2 fails to map very diverged sequences, but this is now being accounted for.
• In --no-temp mode, minimap redirection was causing pangolin to break, now no longer re-direct this output, so appears on screen, but pipeline doesn't break.

pangolin v2.3.8

Release notes

• Removing post hoc test for B.1.214.2 as pangoLEARN model now trained on all 4 sublineages of B.1.214.
• pangolin now explicitly checks for the availability of minimap2, gofasta and snakemake and prints an informative message if they're not there.

pangolin v2.3.6

Release notes

• Adding post hoc test in to explicitly check for lineage P.3

pangolin v2.3.5

Release notes

• Patch for sublineages of B.1.351, now not assigned defaults to B.1.351.

pangolin v2.3.4

Release notes

• Minor release adding post-hoc curation step for lineage B.1.214.2

pangolin v2.3.3

Release notes

• Minor release allowing post hoc curation to handle sublineages of B.1.351

pangolin v2.3.2

Release notes

• Minor release with fix to lineage assignment of P.1 and P.2, explicitly checking for misassignments by model and correct in post hoc check.

pangolin v2.3.0

Release notes

• Introduction of --alignment flag that outputs the aligned fasta file to the output directory rather than the tempdir.
• Speed up of alignment step by switching of datafunk to gofasta, this dependency switched in the environment file (major release tagged as env will need updating with this one).
• Now also piping minimap2 output to gofasta rather than creating an intermediate temp sam file.