Note: This is a redo of PR #232, where pushing my edits produced an unexpected merge commit.
Reviews
[ ] @ConnorChato
[ ] Pull Release Documentation reviewed.
[ ] Test Summary Package reviewed.
[ ] Tests (continuous integration) reviewed.
[x] @TheZetner
[x] Pull Release Documentation reviewed.
[x] Test Summary Package reviewed.
[x] Tests (continuous integration) reviewed.
[x] @AndreaTy
[x] Pull Release Documentation reviewed.
[x] Test Summary Package reviewed.
[x] Tests (continuous integration) reviewed.
Edits
[x] @keaton:
[x] Clarify the difference between a lineage and sublineage change.
[x] Clarify what the node/lineage names mean in the sankey diagrams (ex. cluster_id)
Notes
This is a minor release aimed towards a nextclade dataset upgrade from 2022-10-27 to 2023-01-09 which adds nomenclature for newly designated recombinants XBH - XBP. This release also adds initial support for the detection of "recursive recombination" including XBL and XBN which are recombinants of XBB.
Issue #195: Add bypass to intermission allele ratio for edge cases.
Issue #204: Add special handling for XBB sequenced with ARTIC v4.1 and dropout regions.
Issue #205: Add new column parents_conflict to indicate whether the reported lineages from covSPECTRUM conflict with the reported parental clades from `sc2rf.
v0.7.0 - Recursive Recombinants
Reviews
[ ] @ConnorChato
[x] @TheZetner
[x] @AndreaTy
Edits
Notes
This is a minor release aimed towards a
nextclade
dataset upgrade from2022-10-27
to2023-01-09
which adds nomenclature for newly designated recombinantsXBH
-XBP
. This release also adds initial support for the detection of "recursive recombination" includingXBL
andXBN
which are recombinants ofXBB
.A comprehensive test summary report can be downloaded directly with: ncov-recombinant_v0.6.1_v0.7.0.zip or viewed at the following link once the release is complete.
Documentation
Dataset
Resources
sc2rf
parents_conflict
to indicate whether the reported lineages from covSPECTRUM conflict with the reported parental clades from `sc2rf.XBK
to auto-pass lineages.--gisaid-access-key
tosc2rf
andsc2rf_recombinants
.sc2rf
postprocess.postprocessing.py
was rearranged to have more comprehensive details for auto-pass lineages.XAN
to auto-pass lineages.Plot
rbd_level
to the range of0:12
.--singletons
in favor of--min-cluster-size
to control cluster size in plots.plot
andplot_historical
into one snakemake rule. Also at custom patternplot_NX
(ex.plot_N10
) to adjust min cluster size.Report
report
andreport_historical
into one snakemake rule.Validate
Designated Lineages
XBB.1.5
XBF
XBG
XBH
XBJ
XBK
XBL
XBM
XBN
Proposed Lineages
proposed1305
proposed1340
proposed1425
proposed1440
proposed1444
proposed1576
Continuous Integration
Commits
c279f1e4
docs: add changelog for v0.7.02964b4a1
docs: update notes to include 1576 proposed issuefdc874ab
docs: add test summary package for v0.7.03f3d4438
docs: update docs v0.7.078696b36
script: add bug fix to sc2rf postprocess for #231403777a0
script: lint plotting script2a09c783
script: fix sc2rf postprocess bug in duplicate removald44d5f90
data: add XBP to controls-gisaid4293439c
profile: add controls-gisaid to virusseq builds91d6fb89
defaults: update nextclade dataset to 2023-02-01630b2cd5
resources: update49e6f598
profile: add virusseq profile7e586d1d
script: add extra logic for auto-passing lineages0ebe5e9c
script: fix bug in report where it didn't check that plots existed25b2f243
docs: update developers guide914d933f
defaults: add XBN to controls-gisaid and validation8eaf08a9
data: restore controls-gisaid strain listfa123009
script: defragment plot for 2185f24f695
dataset: update controls-gisaid strain listefc5aab7
defaults: update validation to fix XBH dropout