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CHANGELOG

v0.7.0

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.

Documentation

Dataset

Resources

sc2rf

  • 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.
  • Issue #213: Add XBK to auto-pass lineages.
  • Issue #222: Add new parameter --gisaid-access-key to sc2rf and sc2rf_recombinants.
  • Issue #229: Fix bug where auto-pass lineages are missing when exclude_negatives is set to true.
  • Issue #231: Fix bug where 'null' lineages in covSPECTRUM caused error in sc2rf postprocess.
  • The order of the postprocessing.py was rearranged to have more comprehensive details for auto-pass lineages.
  • Add XAN to auto-pass lineages.

Plot

  • Issue #209: Restrict the palette for rbd_level to the range of 0:12.
  • Issue #218: Fix bug concerning data fragmentation with large numbers of sequences.
  • Issue #221: Remove parameter --singletons in favor of --min-cluster-size to control cluster size in plots.
  • Issue #224: Fix bug where plot crashed with extremely large datasets.
  • Combine plot and plot_historical into one snakemake rule. Also at custom pattern plot_NX (ex. plot_N10) to adjust min cluster size.

Report

  • Combine report and report_historical into one snakemake rule.

Validate

  • Issue #225: Fix bug where false negatives passed validation because the status column wasn't checked.
Designated Lineages
Proposed Lineages

Commits

  • 2964b4a1 docs: update notes to include 1576 proposed issue
  • fdc874ab docs: add test summary package for v0.7.0
  • 3f3d4438 docs: update docs v0.7.0
  • 78696b36 script: add bug fix to sc2rf postprocess for #231
  • 403777a0 script: lint plotting script
  • 2a09c783 script: fix sc2rf postprocess bug in duplicate removal
  • d44d5f90 data: add XBP to controls-gisaid
  • 4293439c profile: add controls-gisaid to virusseq builds
  • 91d6fb89 defaults: update nextclade dataset to 2023-02-01
  • 630b2cd5 resources: update
  • 49e6f598 profile: add virusseq profile
  • 7e586d1d script: add extra logic for auto-passing lineages
  • 0ebe5e9c script: fix bug in report where it didn't check that plots existed
  • 25b2f243 docs: update developers guide
  • 914d933f defaults: add XBN to controls-gisaid and validation
  • 8eaf08a9 data: restore controls-gisaid strain list
  • fa123009 script: defragment plot for 218
  • 5f24f695 dataset: update controls-gisaid strain list
  • efc5aab7 defaults: update validation to fix XBH dropout
  • 5a76f81c sc2rf: update sc2rf to use gisaid access token
  • 84a01cfc script: fix validate bug for #225
  • cc031e37 env: version control all docs dependencies
  • e1c18b91 env: add kaleido for static image export
  • f63a254a docs: update configuration and faq
  • 41c533fd docs: update links in developers guide
  • 71d48037 defaults: update validation values
  • 35a5d1ee script: change slurm job name to basename of conda env
  • 04e425f8 docs: change links to html refs
  • ccda5121 docs: add pipeline definiton example
  • 18e7ae78 docs: remove README content and link to read the docs
  • 5f7ec1a1 docs: rename sphinx pages
  • d9cc87dd workflow: create new pattern plot_NX to customize min cluster size
  • 1c3cc7a4 docs: success with read the docs, fix description include
  • 5921240b env: add sphinx rtd theme
  • cd789917 docs: try read the docs with requirements
  • 6d63bcbf docs: remove sphinx conda too slow
  • 47fe5a54 env: switch git from anaconda to conda-forge channel
  • 7e8c4c6c docs: downgrade sphinx python to 3.8
  • 28e7be0e docs: attempt conda 3 with sphinx readthedocs
  • 985159b6 docs: attempt conda 2 with sphinx readthedocs
  • 7ab1c5d9 docs: attempt conda with sphinx readthedocs
  • 6d7079a8 docs: add sphinx for readthedocs #24
  • 1809dad5 workflow: update validation for new controls-gisaid strains
  • 71c0fb34 script: catch tight layout warnings for #224
  • 690bbd7c resources: update issues
  • 348264b4 resources: add proposed1444 and proposed1576 to breakpoints
  • 3f657060 resources: add XBL and XBM to breakpoints
  • a8528cc0 docs: add development section to README
  • b0446f66 docs: add development section to README
  • 03a65ebf ci: extend miniforge-variant to all jobs for #223
  • f186a1c6 ci: use miniforge-variant to fix #223
  • cb1bda73 script: add intermission ratio bypass for #195
  • c0429ec3 parameter: update nextclade data
  • 2377fce6 script: improve postprocess duplicate reconciliation for lineage matches
  • 6b891c92 resources: add proposed1440 to breakpoints #214
  • 7171dcfd resources: add proposed1425 to breakpoints #212
  • d5a2bf1c resources: add proposed1393 to breakpoints #211
  • 18961b51 script: improve postprocess duplicate reconciliation with multiple strain matches
  • 1d7263f9 resources: add proposed1340 to breakpoints #208
  • 9b06cff6 resources: update validation for controls
  • 762fc77d script: fix postprocess bug in auto-pass parsing
  • ea7cdcaf param: add XBK to resources and voc
  • ccc08dba resources: upgrade sc2rf, upgrade Nextclade #176, update XBG breakpoints #206, parent conflict #205, rbd palette #209
  • c0c9209b script: fix cluster str recode in plot_breakpoints
  • 044040c2 param: add XAN to auto-pass
  • d7e728d0 script: handle numeric strain names for #210
  • c014cfb7 script: hardcode rbd palette range from 0 to 12 for #209
  • 91f4bb05 script: fix missing X parent in lineage_tree for #185
  • f341dd59 ci: switch flake8 repo from gitlab to github
  • dea9eeb3 resources: update XBB validation lineage
  • be32e69e workflow: fix typo in nextclade dataset_dir
  • 575255b8 workflow: move lineage tree to resources as not dependent on nextclade for #185
  • 447b0b8b env: add pango-aliasor for #185
  • 823428a9 param: add XBB_ARTIC alt breakpoints for #204

v0.6.1

Notes

This is a minor bugfix release aimed towards resolving network connectivity errors and catching false positives.

sc2rf

  • Issue #195: Consider alleles outside of parental regions as intermissions (conflicts) to catch false positives.
  • Issue #201: Make LAPIS query of covSPECTRUM optional, to help with users with network connectivity issues. This can be set with the flag lapis: false in builds under the rule sc2rf_recombinants.
  • Issue #202: Document connection errors related to LAPIS and provide options for solutions.

Commits

  • 83ee0139 docs: update changelog for v0.6.1
  • 00fe2fc8 docs: update notes for v0.6.1
  • fa03ea96 workflow: fix bug where rbd_levels log was incorrectly named
  • a281b75c workflow: make lapis optional param for #201 #202
  • 75684b55 docs: update docs
  • 1085ce0e script: postprocess count alleles outside regions as intermissions for #195
  • c11770c1 param: add XAV to auto-pass for #104 #195

v0.6.0

Notes

This is a major release that includes the following changes:

Dataset

  • Issue #168: NULL collection dates and NULL country is implemented.
  • controls was updated to in include 1 strain from XBB for a total of 22 positive controls. The 28 negative controls were unchanged from v0.5.1.
  • controls-gisaid strain list was updated to include XA through to XBE for a total of 528 positive controls. This includes sublineages such as XBB.1 and XBB.1.2 which synchronizes with Nextclade Dataset 2022-10-19. The 187 negatives controls were unchanged from v0.5.1.

Nextclade

  • Issue #176: Upgrade Nextclade dataset to tag 2022-10-27 and upgrade Nextclade to v2.8.0.
  • Issue #193: Use the nextclade dataset sars-cov-2-21L to calculate immune_escape and ace2_binding.

RBD Levels

  • Issue #193: Create new rule rbd_levels to calculate the number of key receptor binding domain (RBD) mutations.

Lineage Tree

  • Issue #185: Use nextclade dataset Auspice tree for lineage hierarchy. Previously, the phylogeny of lineages was constructed from the cov-lineages website YAML. Instead, we now use the tree provided with nextclade datasets, to better synchronize the lineage model with the output.

Rather than creating the output tree in resources/lineages.nwk, the lineage tree will output to data/sars-cov-2_<DATE>/tree.nwk. This is because different builts might use different nextclade datasets, and so are dataset specific output.

sc2rf

  • Issue #179: Fix bug where sc2rf/recombinants.ansi.txt is truncated.
  • Issue #180: Fix recombinant sublineages (ex. XAY.1) missing their derived mutations in the cov-spectrum_query. Previously, the cov-spectrum_query mutations were only based on the parental alleles (before recombination). This led to sublinaeges (ex. XAY.1, XAY.2) all having the exact same query. Now, the cov-spectrum_query will include all substitutions shared between all sequences in the cluster_id.
  • Issue #187: Document bug that occurs if duplicate sequences are present, and the initial validation was skipped by not running scripts/create_profile.sh.
  • Issue #191 and Issue #192: Reduce false positives by ensuring that each mode of sc2rf has at least one additional parental population that serves as the alternative hypothesis.
  • Issue #195: Implement a filter on the ratio of intermissions to alleles. Sequences will be marked as false positives if the number of intermissions (i.e. alleles that conflict with the identified parental region) is greater than or equal to the number of alleles contributed by the minor parent. This ratio indicates that there is more evidence that conflicts with recombination than there is allele evidence that supports a recombinant origin.

Linelist

  • Issue #183: Recombinant sublineages. When nextclade calls a lineage (ex. XAY.1) which is a sublineage of a sc2rf lineage (XAY), we prioritize the nextclade assignment.
  • Issue #193: Add immune-related statistics: rbd_levels, rbd_substitutions, immune_escape, and ace2_binding.

Plot

  • Issue #57: Include substitutions within breakpoint intervals for breakpoint plots. This is a product of Issue #180 which provides access to all substitutions.
  • Issue #112: Fix bug where breakpoints plot image was out of bounds.
  • Issue #188: Remove the breakpoints distribution axis (ex. breakpoints_clade.png) in favor of putting the legend at the top. This significant reduces plotting issues (ex. Issue #112).
  • Issue #193: Create new plot rbd_level.

Validate

Designated Lineages
Proposed Lineages

Commits

  • 2506e907 docs: update changelog and add v0.6.0 testing summary package
  • 0cc421e0 docs: update all contributors
  • cd9b6cbb resources: update issues
  • 0fa2e3c1 docs: update readme
  • 375c3a76 resources: add proposed lineages for #197 #198 #199
  • dad989e7 param: remove BQ.1 from sc2rf mode VOC as its too close to BA.5.3
  • d7cb005f docs: update issue template lineage-validation
  • 1beac97e resources: add XBF to curated breakpoints for #196
  • fae7bfdb script: sc2rf implement intermission allele ratio for #195
  • 89a41265 script: additional manual curation of lineage_tree
  • ebd3ce1f resources: update validation strains for controls-gisaid
  • d8bff572 script: add RBD Level slide to report
  • c1879c1d script: catch errors in rbd_level plotting with no recombinants
  • 63545a08 script: fix bug in linelist with cluster_privates
  • c24a7179 resources: update issues
  • d32d557f docs: update development notes
  • 7f825a41 script: manual fix for CK in lineage_tree
  • fdd6f66d workflow: implement rbd levels for #193
  • 0058dd6e param: upgrade nextclade dataset to 2022-10-27 and reduce breakpoints of XA mode
  • fb062c32 env: upgrade nextclade to v2.8.0
  • 800c1e9c param: experiment with XAJ mode for 191
  • 6958337f env: version control pip to v22.3 on conda-forge
  • 2bf5141b env: change anaconda channel to conda-forge for #170
  • 9b484d3b script: allow NULL dates in metadata for #168 remove breakpoint dist axis for #188 fix breakpoints plot out of bounds for #112
  • 90b153e7 docs: update dev notes
  • 5057814a resources: remove deprecated lineages and geo_resolutions
  • 28c1b8bd resources: update issues and breakpoints
  • 379112b4 profile: update validation values
  • f8f4273c profile: update controls-gisaid to XBE
  • e462cead profile: add XBB.1 to controls
  • c2aca577 profile: increase max jobs in controls-gisaid-hpc
  • eabbed42 param: add more BA.5 sublineages to sc2rf lineages
  • 75e674e0 workflow: implement sublineages for #183
  • 5caaaa4f workflow: use nextclade dataset for phylogeny for #185
  • 732f5eea resources: add XBC.1 to breakpoints for #181
  • 2c1f09a5 resources: add new lineage XAY.1 to curated breakpoints for #178
  • b44e68e1 script: use all substitutions for cov-spectrum for #180 and #57
  • 9d222e1f script: ignore issue 848 when downloading, is manually curated
  • 98c8a912 script: bugfix where sc2rf ansi was truncated for #179
  • 1e29d7ea env: upgrade nextclade and nextclade dataset for #176
  • 409183f5 resources: update breakpoints for proposed1139 #165

v0.5.1

Notes

Workflow

  • Issue #169: AttributeError: 'str' object has no attribute 'name'

Resources

  • Issue #167: Alias key out of date, change source

Validate

Proposed Lineages

Commits

  • 799904eb docs: update CHANGELOG for v0.5.1
  • 1f9cd623 docs: update docs for v0.5.1
  • 43fc4d71 env: update tabulate channel for #169
  • 3b9c3796 env: version control tabulate for #169
  • 5f57bca2 script: update alias url for #167
  • 31647371 docs: update readme hpc section

v0.5.0

Notes

Please check out the v0.5.0 Testing Summary Package for a comprehensive report.

This is a minor release that includes the following changes:

  1. Detection of all recombinants in Nextclade dataset 2022-09-27: XA to XBC.
  2. Create any number of custom sc2rf modes with CLI arguments.

Resources

  • Issue #96: Create newick phylogeny of pango lineage parent child relationships, to get accurate sublineages including aliases.
  • Issue #118: Fix missing pango-designation issues for XAY and XBA.

Datasets

  • Issue #25: Reduce positive controls to one sequence per clade. Add new positive controls XAL, XAP, XAS, XAU, and XAZ.
  • Issue #92: Reduce negative controls to one sequence per clade. Add negative control for 22D (Omicron) / BA.2.75.
  • Issue #155: Add new profile and dataset controls-gisaid. Only a list of strains is provided, as GISAID policy prohibits public sharing of sequences and metadata.

Profile Creation

  • Issue #77: Report slurm command for --hpc profiles in scripts/create_profiles.sh.
  • Issue #153: Fix bug where build parameters metadata and sequences were not implemented.

Nextclade

  • Issue #81: Upgrade Nextclade datasets to 2022-09-27
  • Issue #91: Upgrade Nextclade to v2.5.0

sc2rf

  • Issue #78: Add new parameter max_breakpoint_len to sc2rf_recombinants to mark samples with two much uncertainty in the breakpoint interval as false positives.

  • Issue #79: Add new parameter min_consec_allele to sc2rf_recombinants to ignore recombinant regions with less than this number of consecutive alleles (both diagnostic SNPs and diganostic reference alleles).

  • Issue #80: Migrate sc2rf froma submodule to a subdirectory (including LICENSE!). This is to simplify the updating process and avoid errors where submodules became out of sync with the main pipeline.

  • Issue #83: Improve error handling in sc2rf_recombinants when the input stats files are empty.

  • Issue #89: Reduce the default value of the parameter min_len in sc2rf_recombinants from 1000 to 500.This is to handle XAP and XAJ.

  • Issue #90: Auto-pass select nextclade lineages through sc2rf: XN, XP, XAR, XAS, and XAZ. This requires differentiating the nextclade inputs as separate parameters --nextclade and --nextclade-no-recom.

    XN,XP, and XAR have extremely small recombinant regions at the terminal ends of the genome. Depending on sequencing coverage, sc2rf may not reliably detect these lineages.

    The newly designated XAS and XAZ pose a challenge for recombinant detection using diagnostic alleles. The first region of XAS could be either BA.5 or BA.4 based on subsitutions, but is mostly likely BA.5 based on deletions. Since the region contains no diagnostic alleles to discriminate BA.5 vs. BA.4, breakpoints cannot be detected by sc2rf.

    Similarly for XAZ, the BA.2 segments do not contain any BA.2 diagnostic alleles, but instead are all reversion from BA.5 alleles. The BA.2 parent was discovered by deep, manual investigation in the corresponding pango-designation issue. Since the BA.2 regions contain no diagnostic for BA.2, breakpoints cannot be detected by sc2rf.

  • Issue #95: Generalize sc2rf_recombinants to take any number of ansi and csv input files. This allows greater flexibility in command-line arguments to sc2rf and are not locked into the hardcoded primary and secondary parameter sets.

  • Issue #96: Include sub-lineage proportions in the parents_lineage_confidence. This reduces underestimating the confidence of a parental lineage.

  • Issue #150: Fix bug where sc2rf would write empty output csvfiles if no recombinants were found.

  • Issue #151: Fix bug where samples that failed to align were missing from the linelists.

  • Issue #158: Reduce sc2rf param --max-intermission-length from 3 to 2 to be consistent with Issue #79.

  • Issue #161: Implement selection method to pick best results from various sc2rf modes.

  • Issue #162: Upgrade sc2rf/virus_properties.json.

  • Issue #163: Use LAPIS nextcladePangoLineage instead of pangoLineage. Also disable default filter max_breakpoint_len for XAN.

  • Issue #164: Fix bug where false positives would appear in the filter sc2rf ansi output (recombinants.ansi.txt).

  • The optional lapis parameter for sc2rf_recombinants has been removed. Querying LAPIS for parental lineages is no longer experimental and is now an essential component (cannot be disabled).

  • The mandatory mutation_threshold parameter for sc2rf has been removed. Instead, --mutation-threshold can be set independently in each of the scrf modes.

Linelist

  • Issue #157: Create new parameters min_lineage_size and min_private_muts to control lineage splitting into X*-like.

Plot

  • Issue #17: Create script to plot lineage assignment changes between versions using a Sankey diagram.
  • Issue #82: Change epiweek start from Monday to Sunday.
  • Issue #111: Fix breakpoint distribution axis that was empty for clade.
  • Issue #152: Fix file saving bug when largest lineage has / characters.

Report

  • Issue #88: Add pipeline and nextclade versions to powerpoint slides as footer. This required adding --summary as param to report.

Validate

  • Issue #56: Change rule validate from simply counting the number of positives to validating the fields lineage, breakpoints, parents_clade. This involves adding a new default parameter expected for rule validate in defaults/parameters.yaml.
Designated Lineages
Proposed Lineages

Pull Requests

  • pull/113 docs: add issues template for lineage validation

Commits

  • b48ad6d7 docs: fix CHANGELOG pr
  • 04b17918 docs: update readme and changelog
  • 72dd5a8f docs: add testing summary package for v0.4.2 to v0.5.0
  • 558f7d79 resources: fix breakpoints for XAE #122
  • 91e5843b script: bugfix sc2rf ansi output for #164
  • 9bc13639 docs: update issues and validation table order
  • b63520e5 script: implement lineage check in dups for #117 #161
  • 901898da sc2rf updates for #158 #161 #162 #163
  • 96fa6af1 dataset: update controls-gisaid strain list and validation
  • 84466a10 workflow: new param dup_method for #161
  • 9ca0c71e script: implement duplicate reconciliation for #161
  • 112ea684 param: upgrade nextclade dataset for #159
  • 859b92c8 script: add more detail to validate table for failing samples
  • 5e285912 script: add param --min-link-size to compare_positives
  • bd01a5e4 workflow: added failed validate output to rule log
  • 8e5b90fb workflow: don't use metadata for sc2rf_recombinants when exclude_negatives is true
  • cdf45407 param: add new params min-lineage-size and min-private-muts for #157
  • bc04fddf workflow: update validation strains for #155
  • 6aa95221 param: fix typo of missing --mutation-threshold
  • 25df848c param: remove param mutation_threshold as universal param for sc2rf
  • 46d2ee95 dataset: remove false positive LC0797902 from negative controls
  • b106b9d1 profile: change default hpc jobs from 2 to 10
  • d6d02721 workflow: update validation table
  • d308d54b script: fix node ordering in compare_positives
  • ea65c6ff ci: remove GISAID workflow for #154
  • 122e579c ci: test storing csv files as secrets for #154
  • d281add4 ci: experiment with secrets with test data for #154
  • 1d5406f5 script: generalize compare_positives to use other lineage columns
  • ffd4f159 scripts: fix bug where metadata and sequences param were not implemented for #153
  • 7974860a resources: special handling of proposed808 issues and breakpoints for #99
  • d0e3f41a script: fix file saving bug in report for #152
  • f7d3157b script: fix file saving bug in plot for #152
  • f9931bb3 script: fix missing samples in sc2rf output for #151
  • 18b94df5 script: force sc2rf to always output csvfile headers for #150
  • e1f14dfe resources: update breakpoints for proposed808 #99
  • 35aaa922 resources: update breakpoints for XA - XAZ
  • 05cba895 resources: update breakpoints for XV #130
  • 1b0a02bf resources: add gauntlet samples (all XA*) to validation
  • 29c7798d param: add XAR to sc2rf auto-pass for 106
  • 0e6b413e docs: change next ver from v0.4.3 to v0.5.0
  • f8197e80 workflow: fix bug in rule validate where path was hard-coded
  • abb4dec6 resources: update breakpoints for XAA #126
  • d012b936 resources: update breakpoints for XAG and XAH for #120 and #121
  • d389e048 param: add new XAJ mode for sc2rf for #117
  • be853ac1 scripts: update rule validate for #56
  • a02b4deb docs: add issues template for lineage validation #113
  • 1b3cb780 script: fix bug of missing issues for #118
  • 82d9ce32 docs: update validation release notes
  • 1b705a6a resources: update XAU breakpoints for #103
  • 18021fe3 docs: add XAQ issue #107 to release notes
  • 7ca8f06f docs: add XAQ issue #107 to release notes
  • e9d8f905 docs: add issue #111 to release notes
  • a638835a script: fix bug in plot_breakpoints when axis empty for #111
  • ba7ec30c resources: update breakpoints for XAP #108
  • d3952e44 docs: fix typo in relesae notes
  • d56956d6 docs: add issues #86 and #87 to release notes
  • 00a706a8 script: remove redundant --clades arg in sc2rf bash script
  • 378eea62 param: add new sc2rf modes XB and proposed808 for #98 and #99
  • bb802647 docs: add issue #17 to release notes
  • b6688c86 env: add plotly to conda env and control all versions
  • adc6777e script: improve directory creation in compare positives
  • 15a1fc04 script: add breakpoint axis label for #97
  • f256a75f docs: add notes for v0.4.3
  • c3785fa0 env: upgrade csvtk to v0.24.0
  • 7936e0ef param: fix typo in mode omicron_omicron
  • d014d0a1 param: revert XAS mode to default for #86
  • ea83d78e script: fix bug in postprocess where max_breakpoint_len was not checked
  • ab030e21 param: add new XAS mode to default sc2rf runs for #86
  • 6ccd0aa8 workflow: first draft of pango lineage tree for #96
  • 9d2382cb workflow: add param fix for postprocess inputs
  • 93007726 script: fix cli --clades arg parsing for scr2rf.sh
  • bed29fdb script: add new csv col alleles to sc2rf
  • bd681d5e workflow: generalize sc2rf_recombinants inputs for #95
  • 0315ffd6 docs: update development docs
  • 70111447 resources: update breakpoints and issues
  • 076e14bb dataset: reduce controls to one sequence per clade for #25,92
  • 77d2210d workflow: update rules for #46, #88, #89, #90
  • d84205a0 script: add new param auto_pass for #90
  • 99b895a4 params: update params for #46, #89, #90
  • 3e3d1022 script: add pipeline version to report for #88
  • 2e6ac558 script: remove sc2rf_ver col from summary for #80
  • 18c35940 env: upgrade nextclade to v2.5.0 for #91
  • a67e1159 workflow: autopass XAS through sc2rf for #86
  • 2e16dac5 resources: update breakpoints and mutations
  • a7026450 workflow: upgrade nextclade dataset to 2022-08-23 for #81
  • 53fb4a8a workflow: re-add sc2rf as subdirectory for #80
  • 4b8b3fab workflow: remove sc2rf submodule again
  • b650e562 workflow: add sc2rf as subdirectory for #80
  • 073f3b94 workflow: remove sc2rf as submodule
  • 5ab5c1b5 resources: updated curated breakpoints
  • 5635b872 resources: update issues
  • 78e1f064 script: change epiweek to start on Sundary (cdc) for #82
  • 37f40480 script: add tables to compare positives between versions for #17
  • 8eef7548 script: create new script to compare positives between versions
  • ebf1e222 script: compare linelists from different versions for #17
  • 8401c353 workflow: add new param max_breakpoint_len for #78
  • 8bbcc041 script: report slurm command for --hpc profiles for #77
  • c40a6791 workflow: restrict config rules to one thread
  • c2b1ea57 script: revert unpublished lineages for #76
  • dbe359c8 resources: add 882 to breakpoints

v0.4.2

Notes

This is a minor bug fix and enhancement release with the following changes:

Linelist

  • Issue #70: Fix missing sc2rf version from recombinant_classifier_dataset
  • Issue #74: Correctly identify XN-like and XP-like. Previously, these were just assigned XN/XP regardless of whether the estimated breakpoints conflicted with the curated ones.
  • Issue #76: Mark undesignated lineages with no matching sc2rf lineage as unpublished.

Plot

  • Issue #71: Only truncate cluster_id while plotting, not in table generation.
  • Issue #72: For all plots, truncate the legend labels to a set number of characters. The exception to this are parent labels (clade,lineage) because the full label is informative.
  • Issue #73, #75: For all plots except breakpoints, lineages will be defined by the column recombinant_lineage_curated. Previously it was defined by the combination of recombinant_lineage_curated and cluster_id, which made cluttered plots that were too difficult to interpret.
  • New parameter --lineage-col was added to scripts/plot_breakpoints.py to have more control on whether we want to plot the raw lineage (lineage) or the curated lineage (recombinant_lineage_curated).

Commits

  • 8953ef03 docs: add CHANGELOG for v0.4.2
  • 7ec5ccc6 docs: add notes for v0.4.2
  • 1b3b1f1d script: restore column name to recombinant_classifer_dataset
  • 901caf98 script: restore recombinant_lineage_curated of -like lineages
  • d6be9611 script: change internal delim of classifier for #70
  • cdb4a78a script: fix recombinant_classifier missing sc2rf for #70
  • bf7a4e57 script: mark undesignated lineages with no matching sc2rf lineage as unpublished for #76
  • 46f6d754 workflow: update linelists and plotting for #74 and #75
  • c03dd3be script: don't split largest by cluster id for #73
  • e9802e79 script: majority of plots will not split by cluster_id for #73
  • bafb38fb script: fix cluster ID truncation for issue #71
  • ab712593 resources: curate and test breakpoints for proposed895

v0.4.1

Notes

This is a minor bug fix release with the following changes:

  • Issue #63: Remove usher and protobuf from the conda environment.
  • Issue #68: Remove ncov as a submodule.
  • Issue #69: Remove 22C and 22D from sc2rf/mapping.csv and sc2rf/virus_properties.json, as these interfere with breakpoint detection for XAN.

Commits

  • 88650696 docs: add CHANGELOG for v0.4.1
  • 00a2eec3 docs: add notes for v0.4.1
  • d74a81d3 sc2rf: revert 22C and 22D clade addition
  • 7b662940 env: remove usher for issue #63
  • adf92399 submodule: remove ncov for issue #68
  • 0790aa04 docs: update CHANGELOG for v0.4.0

v0.4.0

Notes

General

v0.4.0 has been trained and validated on the latest generation of SARS-CoV-2 Omicron clades (ex. 22A/BA.4 and 22B/BA.5). Recombinant sequences involving BA.4 and BA.5 can now be detected, unlike in v0.3.0 where they were not included in the sc2rf models.

v0.4.0 is also a major update to how sequences are categorized into lineages/clusters. A recombinant lineage is now defined as a group of sequences with a unique combination of:

  • Lineage assignment (ex. XM)
  • Parental clades (ex. Omicron/21K,Omicron/21L)
  • Breakpoints (ex. 17411:21617)
  • NEW: Parental lineages (ex. BA.1.1,BA.2.12.1)

Novel recombinants (i.e. undesignated) can be identified by a lineage assignment that does not start with X* (ex. BA.1.1) or with a lineage assignment that contains -like (ex. XM-like). A cluster of sequences may be flagged as -like if one of the following criteria apply:

  1. The lineage assignment by Nextclade conflicts with the published breakpoints for a designated lineage (resources/breakpoints.tsv).

    • Ex. An XE assigned sample has breakpoint 11538:12879, which conflicts with the published XE breakpoint (ex. 8394:12879). This will be renamed XE-like.

  2. The cluster has 10 or more sequences, which share at least 3 private mutations in common.

    • Ex. A large cluster of sequences (N=50) are assigned XM. However, these 50 samples share 5 private mutations T2470C,C4586T,C9857T,C12085T,C26577G which do not appear in true XM sequences. These will be renamed XM-like. Upon further review of the reported matching pango-designation issues (460,757,781,472,798), we find this cluster to be a match to proposed798.

The ability to identify parental lineages and private mutations is largely due to improvements in the newly released nextclade datasets, , which have increased recombinant lineage accuracy. As novel recombinants can now be identified without the use of the custom UShER annotations (ex. proposed771), all UShER rules and output have been removed. This significantly improves runtime, and reduces the need to drop non-recombinant samples for performance. The result is more comparable output between different dataset sizes (4 samples vs. 400,000 samples).

Note! Default parameters have been updated! Please regenerate your profiles/builds with:

scripts/create_profile.sh --data data/custom

Datasets

  • Issue #49: The tutorial lineages were changed from XM,proposed467, miscBA1BA2Post17k, to XD, XH, XAN. The previous tutorial sequences had genome quality issues.
  • Issue #51: Add XAN to the controls dataset. This is BA.2/BA.5 recombinant.
  • Issue #62: Add XAK to the controls dataset. This is BA.2/BA.1 VUM recombinant monitored by the ECDC.

Nextclade

  • Issue #46: nextclade is now run twice. Once with the regular sars-cov-2 dataset and once with the sars-cov-2-no-recomb dataset. The sars-cov-2-no-recomb dataset is used to get the nucleotide substitutions before recombination occurred. These are identified by taking the substitutions column, and excluding the substitutions found in privateNucMutations.unlabeledSubstitutions. The pre-recombination substitutions allow us to identify the parental lineages by querying cov-spectrum.
  • Issue #48: Make the exclude_clades completely optional. Otherwise an error would be raised if the user didn't specify any.
  • Issue #50: Upgrade from v1.11.0 to v2.3.0. Also upgrade the default dataset tags to 2022-07-26T12:00:00Z which had significant bug fixes.
  • Issue #51: Relax the recombinant criteria, by flagging sequences with ANY labelled private mutations as a potential recombinant for further downstream analysis. This was specifically for BA.5 recombinants (ex. XAN) as no other columns from the nextclade output indicated this could be a recombinant.
  • Restrict nextclade output to fasta,tsv (alignment and QC table). This saves on file storage, as the other default output is not used.

sc2rf

  • Issue #51: sc2rf is now run twice. First, to detect recombination between clades (ex. Delta/21J & Omicron/21K). Second, to detect recombination within Omicron (ex. Omicron/BA.2/21L & Omicron/BA.5/22B). It was not possible to define universal parameters for sc2rf that worked for both distantly related clades, and the closely related Omicron lineages.
  • Issue #51: Rename parameter clades to primary_clades and add new parameter secondary_clades for detecting BA.5.
  • Issue #53: Identify the parental lineages by splitting up the observed mutations (from nextclade) into regions by breakpoint. Then query the list of mutations in https://cov-spectrum.org and report the lineage with the highest prevalence.
  • Tested out --enable-deletions again, which caused issues for XD. This confirms that using deletions is still ineffective for defining breakpoints.
  • Add B.1.631 and B.1.634 to sc2rf/mapping.tsv and as potential clades in the default parameters. These are parents for XB.
  • Add B.1.438.1 to sc2rf/mapping.tsv and as a otential clade in the default parameters. This is a parent for proposed808.
  • Require a recombinant region to have at least one substitution unique to the parent (i.e. diagnostic). This reduces false positives.
  • Remove the debugging mode, as it produced overly verbose output. It is more efficient to rerun manually with custom parameters tailored to the kind of debugging required.
  • Change parent clade nomenclature from Omicron/21K to the more comprehensive Omicron/BA.1/21K. This makes it clear which lineage is involved, since it's not always obvious how Nextclade clades map to pango lineages.

UShER

  • Issue #63: All UShER rules and output have been removed. First, because the latest releases of nextclade datasets (tag 2022-07-26T12:00:00Z) have dramatically improved lineage assignment accuracy for recombinants. Second, was to improve runtime and simplicity of the workflow, as UShER adds significantly to runtime.

Linelist

  • Issue #30: Fixed the bug where distinct recombinant lineages would occasionally be grouped into one cluster_id. This is due to the new definition for recombinant lineages (see General) section, which now includes parental lineages and have sufficient resolving power.
  • Issue #46: Added new column parents_subs, which are the substitutions found in the parental lineages before recombination occurred using the sars-cov-2-no-recomb nextclade dataset. Also added new columns: parents_lineage, parents_lineage_confidence, based on querying cov-spectrum for the substitutions found in parents_subs.
  • Issue #53: Added new column cov-spectrum_query which includes the substitutions that are shared by ALL sequences of the recombinant lineage.
  • Added new column cluster_privates which includes the private substitutions shared by ALL sequences of the recombinant lineage.
  • Renamed parents column to parents_clade, to differentiate it from the new column parents_lineage.

Plot

  • Issue #4, Issue #57: Plot distributions of each parent separately, rather than stacking on one axis. Also plot the substitutions as ticks on the breakpoints figure.
v0.3.0 v0.4.0
breakpoints_clade_v0.3.0 breakpoints_clade_v0.4.0
  • Issue #46: Plot breakpoints separately by clade and lineage. In addition, distinct clusters within the same recombinant lineage are noted by including their cluster ID as a suffix. As an example, please see XM (USA) and X (England) below. Where the lineage is the same (XM), but the breakpoints differ, as do the parental lineages (BA.2 vs BA.2.12.1). These clusters are distinct because XM (England) lacks substitutions occurring around position 20000.
Clade Lineage
breakpoints_clade breakpoints_clade
  • Issue #58: Fix breakpoint plotting from all lineages to just those observed in the reporting period. Except for the breakpoint plots in plots_historical.
  • Issue #59: Improved error handling of breakpoint plotting when a breakpoint could not be identified by sc2rf. This is possible if nextclade was the only program to detect recombination (and thus, we have no breakpoint data from sc2rf).
  • Issue #64: Improved error handling for when the lag period (ex. 4 weeks) falls outside the range of collection dates (ex. 2 weeks).
  • Issue #65: Improved error handling of distribution plotting when only one sequence is present.
  • Issue #67: Plot legends are placed above the figure and are dynamically sized.
v0.3.0 v0.4.0
lineages_output_v0.3.0 lineages_output_v0.4.0

Report

  • Issue #60: Remove changelog from final slide, as this content did not display correctly
  • Issue #61: Fixed bug in the report.xlsx where the number of proposed and unpublished recombinant lineages/sequences was incorrect.

Validation

  • Issue #58: New rule (validate) to validate the number of positives in controlled datasets (ex. controls, tutorials) against defaults/validation.tsv. If validation fails based on an incorrect number of positives, the pipeline will exit with an error. This is to make it more obvious when results have changed during Continuous Integration (CI)

Commits

  • c027027b docs: remove dev notes
  • 77d9f01b ci: remove unit test workflow
  • 574f8c15 docs: update instructions in README
  • 79b61fe2 ci: remove unit tests
  • 3d53ebd2 docs: update notes for v0.4.0
  • b968dc6d script: add more subs columns to lineages linelist
  • 75477ec4 script: adjust lag epiweek by 1 when overlaps
  • 20409f5c sc2rf: mapping change 22C to BA.2.12.1 and add 22D
  • 432b6b79 docs: add breakpoints lineage output for v0.4.0
  • 4fbde4b9 docs: add breakts output image to compare v0.3.0 and v0.4.0
  • af2f25d3 docs: add lineage output image for v0.4.0 to compare
  • 5615f113 docs: add lineage output image for v0.3.0 to compare
  • 57a08096 profile: adjust plotting min and max dates for tutorial
  • 4226c85b script: mark nextclade recombinants unverified by sc2rf as false positives
  • d6700e7a docs: rearrange sections in README
  • 7f773ba7 docs: update report and slides images and links
  • 3599a7f4 script: don't use proposed* lineages from sc2rf as consensus lineage
  • 76106b50 docs: add new image for lineages plot
  • 86c2fa2e docs: update README and images
  • 488ea6c7 script: dynamic legends for #67
  • bec01845 script: move plot legend to top for #67
  • 42d1281b script: make sure X*-like lineages have proposed status
  • 230f9495 resources: update issues
  • 3c2f4c84 script: detect novel recombinants based on private mutations
  • d9e279be resources: update breakpoints for XAF and XAG
  • 2d070cb2 script: improve linelist efficiency for assigning cluster ids
  • b65437f2 script: add create_logger function to general functions import
  • 489154f6 sc2rf: explicitly call variables _primary and _secondary
  • 8f464a14 script: simplify extra columns for summary script
  • 30f90443 workflow: formally run sc2rf in primary/secondary mode in parallel
  • 6688c828 defaults: restore validation counts for XN and XP
  • 043b691e script: add special processing for XN and XP
  • 939cc967 script: only adjust lineage status in linelist if positive
  • 28d91363 dataset: update tutorial strains for #49
  • 09e53a94 workflow: remove usher for #63
  • 22c63de0 workflow: add XAK to controls for Issue #62
  • 342fa2a3 script: create separate slides for designated, proposed, and unpublished for issue #61
  • 84c9b57d script: create separate plots for designated, proposed, and unpublished for issue #61
  • 81c58931 script: if lineage is proposed* use as curated lineage rather than cluster_id
  • 2db6100b ci: fix typo in profile creation job names
  • 18102431 script: remove changelog from report slides for issue #60
  • b7784b30 docs: use new breakpoints path for README
  • 66ee7d1d nextclade: upgrade datasets to tag 2022-07-26 for issue #50
  • 7880327c ci: don't trigger pipeline on images changes
  • e8c71171 docs: update breakpoints images
  • e13138e8 script: rename NA to Unknown parent when plotting breakpoints
  • fc1b6129 script: remove unneeded constants in plot
  • 77d3614a dataset: change controls proposed771 to XAN
  • f2d72330 script: catch empty plot when using tight_layout for breakpoints
  • b55dbe95 workflow: include unpublished in positive status for rule validate
  • 557295b5 script: plotting catch when breakpoints are NA
  • 2306305d profile: set exclusions for tutorial to default
  • c049ccba resource: update curated breakpoints
  • 218bab52 env: upgrade nextclade to v2.3.0 for issue #50
  • a9ea0bd4 workflow: fix typo in rule validate that hard-coded controls
  • cf613c34 workflow: control breakpoint plotting by clusters file
  • 0d4b50a4 resource: update breakpoints figures
  • 6520457a script: plot subs along with breakpoints for issue #57
  • 8110faa7 script: create a plot for cluster_id mostly for breakpoint plotting
  • 6f02f09c script: for plot import function categorical_palette
  • 1f6195df profile: by default do not retry jobs
  • 2842a4f9 workflow: add rule validate for issue #56
  • 693b07df script: empty df catching in plot breakpoints
  • 12567fde workflow: classify any sequence with unlabeled private mutations as a potential positive
  • 534ac899 docs: add more comments to summary script
  • 82b6a696 script: fix bug in parent palette for plot breakpoints
  • 42510719 config: remove explicit conda activation in slurm script and profiles
  • ab44e5d7 docs: update readme contributors
  • e8e2b134 dataset: upgrade nextclade dataset
  • 086768c7 parameters: restrict breakpoints and parents to 10 for sc2rf
  • 83af3a73 sc2rf: output NA for false positives breakpoints
  • 4baee0de script: catch empty dataframe in script plot
  • 1dc84bf6 profile: adjust plot end date for positive controls
  • be431cdf workflow: restrict nextclade clades again
  • 76e31f68 resources: add breakpoints by clade
  • 07d96a1e workflow: fix bug in plot_historical
  • 2086b254 sc2rf: update lineage mapping
  • 0d911b20 env: reorganize dependencies
  • c165074b workflow: separate plot_breakpoints into separate script
  • 0497dffd profile: controls-negative include false positives
  • 8bb41c45 script: add separate report slides for clade/lineage parent breakpoints
  • 411bc235 workflow: remove subtree params and add secondary clades
  • f80386aa sc2rf: catch empty secondary csv
  • 6d1b03e0 sc2rf: add optional secondary csv for #51
  • a629eb06 workflow: detect recombination with BA.5 for #51
  • c44b468a env: remove plotly and kaleido from env
  • a485215d dataset: add proposed771 to controls for #51
  • eba827a9 script: define lineages by parental lineages for #46
  • d6319bad workflow: relax nextclade exclusion filter for #48
  • fb7a0a4f env: upgrade nextclade to v2.2.0 for #50
  • 31ec45be resources: update breakpoints parents nomenclature
  • 7f00564d (unverified) sc2rf,postprocess: add unique_subs to output
  • 3e3e46c2 workflow: implement cov-spectrum query to identify parent lineages
  • 041de538 workflow: customize nextclade to run with our without recombinant dataset
  • 7acc598f script: remove edges from stacked bar plots for issue #43
  • ab589bb7 docs: add mark horsman for ideas and design
  • 151e481d bug: fix svg font export for issues #42
  • b34c1452 bug: fix ouput typo in issues_download
  • 601a0c7a resources: also output svg for issues breakpoints
  • a2a8b00d workflow: add plotting issues breakpoints to rule issues_download
  • 5a5a2f41 resources: update breakpoints plot
  • 2113f6f9 script: plot breakpoints of curate lineages in resources
  • 5f4b901d docs: add new breakpoints image to readme
  • bfdf2191 workflow: cleanup Thumbs
  • 869f3b4e script: add breakpoints as a plot and report slide
  • e988f251 bug: fix missing rule_name for _historical
  • 8bc6aef4 env: add plotly and kaleido to env
  • 066e0c00 resources: add 781 789 798 to curated breakpoints
  • 4ff587c5 resources: update issues and curated breakpoints
  • cc146425 docs: add instructions for updating conda env
  • 8592a156 bug: fix usher_collapse metadata output to allow for hCoV-19 prefix
  • 9ea4f1b3 docs: add --recurse-submodules instruction to updating

v0.3.0

Notes

Major Changes

  1. Default parameters have been updated! Please regenerate your profiles/builds with:

    bash scripts/create_profile.sh --data data/custom

  2. Rule outputs are now in sub-directories for a cleaner results directory.

  3. The in-text report (report.pptx) statistics are no longer cumulative counts of all sequences. Instead they, will match the reporting period in the accompanying plots.

Bug Fixes

  1. Improve subtree collapse effiency (#35).
  2. Improve subtree aesthetics and filters (#20).
  3. Fix issues rendering as float (#29).
  4. Explicitly control the dimensions of plots for powerpoint embedding.
  5. Remove hard-coded extra_cols (#26).
  6. Fix mismatch in lineages plot and description (#21).
  7. Downstream steps no longer fail if there are no recombinant sequences (#7).

Workflow

  1. Add new rule usher_columns to augment the base usher metadata.
  2. Add new script parents.py, plots, and report slide to summarize recombinant sequences by parent.
  3. Make rules plot and report more dynamic with regards to plots creation.
  4. Exclude the reference genome from alignment until faToVcf.
  5. Include the log path and expected outputs in the message for each rule.
  6. Use sub-functions to better control optional parameters.
  7. Make sure all rules write to a log if possible (#34).
  8. Convert all rule inputs to snakemake rule variables.
  9. Create and document a create_profile.sh script.
  10. Implement the --low-memory mode parameter within the script usher_metadata.sh.

Data

  1. Create new controls datasets:

    • controls-negatives
    • controls-positives
    • controls

  2. Add versions to genbank_accessions for controls.

Programs

  1. Upgrade UShER to v0.5.4 (possibly this was done in a prior ver).
  2. Remove taxonium and chronumental from the conda env.

Parameters

  1. Add parameters to control whether negatives and false_positives should be excluded:

    • exclude_negatives: false
    • false_positives: false

  2. Add new optional param max_placements to rule linelist.

  3. Remove --show-private-mutations from debug_args of rule sc2rf.

  4. Add optional param --sc2rf-dir to sc2rf to enable execution outside of sc2rf dir.

  5. Add params --output-csv and --output-ansi to the wrapper scripts/sc2rf.sh.

  6. Remove params nextclade_ref and custom_ref from rule nextclade.

  7. Change --breakpoints 0-10 in sc2rf.

Continuous Integration

  1. Re-rename tutorial action to pipeline, and add different jobs for different profiles:

    • Tutorial
    • Controls (Positive)
    • Controls (Negative)
    • Controls (All)

Output

  1. Output new _historical plots and slides for plotting all data over time.

  2. Output new file parents.tsv to summarize recombinant sequences by parent.

  3. Order the colors/legend of the stacked bar plots by number of sequences.

  4. Include lineage and cluster id in filepaths of largest plots and tables.

  5. Rename the linelist output:

    • linelist.tsv
    • positives.tsv
    • negatives.tsv
    • false_positives.tsv
    • lineages.tsv
    • parents.tsv

  6. The report.xlsx now includes the following tables:

    • lineages
    • parents
    • linelist
    • positives
    • negatives
    • false_positives
    • summary
    • issues

Pull Requests

  • pull/19 docs: add lenaschimmel as a contributor for code

Commits

  • 2f8b498a docs: update changelog for v0.3.0
  • 0486d3be docs: add updating section to readme for issue #33
  • e8eda400 resources: updates issues with curate breakpoints
  • 12e3700f bug: catch empty dataframe in plot
  • d1ccca2a workflow: first successful high-throughput run
  • cd741a10 workflow: add new rules plot_historical and report_historical
  • c2cc1380 env: remove openpyxl from environment
  • 7dc7c039 workflow: remove rule report_redact #31
  • 9ca5f822 script: rearrange merge file order in summary
  • aa28eb9f workflow: create new rule report_redact for #31
  • 4748815d env: add openpyxl to environment for excel parsing in python
  • 0060904a script: template duplicate labelling in usher_collapse for later
  • a82359a7 data: add accession versions to controls metadata
  • af7341aa data: add accession versions to controls metadata
  • d860a4c8 workflow: add new rule usher_columns to augment the base usher metadata
  • 2511673d improve subtree collapse effiency (#35) and output aesthetics (#20)
  • 1e81be3b bug: remove non-existant param --log in rule usher_metadata
  • 02198b4c script: add logging to usher_collapse
  • d40d3d78 ci: don't run pipeline just for images changes
  • b880d9c8 docs: update powerpoint image to proper ver
  • 2d6514a0 docs: update demo excel and slides with links and content
  • 59c24ffe bug: fix typo that prevented low_memory_mode from activating
  • 4d94df1d bug: continue supply missing build param to params functions
  • c16c3377 bug: supply missing build param to _params_linelist
  • c31c2204 docs: remove plotting data table from FAQ
  • 5461cbf2 docs: describe how to include more custom metadata columns
  • 7295c8c0 script: implement low memory mode within usher_metadata script
  • 6588f619 workflow: restore original config merge logic
  • ae96cf3d docs: rearrange sections in README
  • e99cdef9 docs: add tips for speeding up usher in FAQ
  • 753d1e1d resources: add proposed759 to curated breakpoints
  • 1ea5610e docs: change troubleshooting section to FAQ
  • 42152710 workflow: add logging to sc2rf_recombinants for issue #34
  • ca930fe3 bug: fix status of designated recombinants missed by sc2rf (XB)
  • 2c6102a6 script: in plotting data replace counts that are empty string with 0
  • 0c7fa988 docs: tidy up comments in default parameters.yaml
  • 43c61d43 bug: fix sc2rf postprocessing bug where sequences with only parent were missing filtered regions
  • 6a00c866 ci: split jobs by profile for testing profile creation (#27)
  • aeabf009 ci: add new action profile_creation to test script create_profile.sh
  • 9a6758e2 add controls section to README
  • ef250a22 script: add -controls suffix to profiles created with --controls param
  • 150a3e17 docs: update troubleshooting section
  • 90b406c8 script: remove --partition flag to scripts/slurm.sh
  • a0c6ece2 docs: update google drive link to example slides
  • a37afeea docs: update instructions for create_profile.sh
  • f9d050d2 add execute permissions to scripts
  • 38b5b422 bug: use a full loop to check issue formatting
  • 307b4f67 catch issues list when converting to str
  • 639f8c26 bug: fix issues rendering as float in tables for issue #29
  • 35ea4be1 remove param --sc2rf-dir from scripts/sc2rf.sh
  • 5a2a9520 docs: update images for excel and powerpoint
  • 3ae737d5 env: comment out yarn which is a dev dependency
  • 3842e898 improve logging in create_profile
  • 84c684ca workflow: separate profiles for controls,controls-positive,controls-negative
  • ad5e8e4b limit missing strains output from create_profile
  • a4898ecf docs: update development notes
  • 34ee2fff docs: add links to contributors plugins
  • b6b0c999 revert to automated all-contributors
  • e1a248f8 add @yatisht and @AngieHinrichs to credits for usher
  • e3f432c4 start adding contributors
  • 862757bd docs: create .all-contributorsrc [skip ci]
  • a0532792 docs: update README.md [skip ci]
  • 6e67e73f update unpublished regex to solve #21
  • 5ba6b37b remove taxonium and chronumental from env
  • 2a5fc627 add artifacts for all pipelines
  • 664b2e9b fix trailing whitespace in metadata
  • eada2fa3 fix negative controls metadata
  • 9aecd69a fix plot dimensions for pptx embed
  • 657e8838 fix outdir for linelist
  • 6fb389dc fix input type for controls build
  • 8ed69ce0 upload tutorial pptx as artifact
  • c6e647d2 update ci profile for test action
  • 19cdb8ed lint pipeline
  • 22e3aa6b split controls action into positives,negatives,and all
  • 33491320 rename action Tutorial to Pipeline
  • da2890d6 fix profile in install action
  • 8a4d4fbb lint all files
  • b167ea45 update readme with profile creation instructions
  • 4d2848b9 add script to generate new profiles and builds
  • 407f8aba checkpoint before auto-generating builds
  • ccb3471b add new negatives dataset
  • 964a22f8 (broken) script overhaul
  • 1f1ca1b4 add param --sc2rf-dir to allow execution outside of main directory
  • 21541f02 add exclude_negatives and exclude_false_positives to parameters
  • 0b5854a2 update docs
  • 58b6396a split controls data into positives and negatives
  • 11f9f6a4 consolidate positives and negatives profiles into controls
  • 581255c8 generalize hpc profiles
  • 1e2a70a4 update HPC instructions in README
  • a18b19e3 (broken) add negatives data and profile
  • 11817639 (broken) make plots and report dynamic
  • e833d151 create tutorial-hpc profile
  • c4ac5699 remove redundant profile laptop
  • c5107017 remove ci profile
  • 4be07e79 actually rename pipeline to tutorial
  • 89c4d6b5 rename pipeline action to tutorial
  • 7614b399 exclude alpha beta gamma by default from Nextclade
  • d2c2461c update dev docs
  • f9368d11 remove proposed636 which is now XZ
  • 4fbd0ce4 add XAA and XAB to resources
  • 65efd145 add xz to resources
  • f3641b19 add parents slide to report and excel
  • 4e25f665 add new script parents to summarize recombinants by parent
  • 0decd47a catch when no designated sequences are present
  • 189fbb2a update resources breakpoints
  • 3c5b4965 update sc2rf with new logic for terminal deletions
  • e37d68d9 update issues and breakpoints
  • 761d41bf use date in changelog for report
  • 3c486dbc add zip to environment
  • 1ff37195 add more info about system config

v0.2.1

Notes

Params

  1. New optional param motifs for rule sc2rf_recombinants.
  2. New param weeks for new rule plot.
  3. Removed prev_linelist param.

Output

  1. Switch from a pdf report to powerpoint slides for better automation.
  2. Create summary plots.
  3. Split report rule into linelist and report.
  4. Output svg plots.

Workflow

  1. New rule plot.
  2. Changed growth calculation from a comparison to the previous week to a score of sequences per day.
  3. Assign a cluster_id according to the first sequence observed in the recombinant lineage.
  4. Define a recombinant lineage as a group of sequences that share the same:
    • Lineage assignment
    • Parents
    • Breakpoints or phylogenetic placement (subtree)
  5. For some sequences, the breakpoints are inaccurate and shifted slightly due to ambiguous bases. These sequences can be assigned to their corresponding cluster because they belong to the same subtree.
  6. For some lineages, global prevalence has exceeded 500 sequences (which is the subtree size used). Sequences of these lineages are split into different subtrees. However, they can be assigned to the correct cluster/lineage, because they have the same breakpoints.
  7. Confirmed not to use deletions define recombinants and breakpoints (differs from published)?

Programs

  1. Move sc2rf_recombinants.py to postprocess.py in ktmeaton fork of sc2rf.
  2. Add false positives filtering to sc2rf_recombinants based on parents and breakpoints.

Docs

  1. Add section Configuration to README.md.

Commits

  • c2369c75 update CHANGELOG after README overhaul
  • 9c8a774e update autologs to exclude first blank line in notes
  • 2a8a7af5 overhaul README
  • 9c2bd2f5 change asterisks to dashes
  • 46d4ec81 update autologs to allow more complex notes content
  • a01a903c split docs into dev and todo
  • 23e8d715 change color palette for plotting
  • 785b8a19 add optional param motifs for sc2rf_recombinants
  • d1c1559e restore pptx template to regular view
  • 6adc5d32 add seaborn to environment
  • 35a04471 add changelog to report pptx
  • 99e98aa7 add epiweeks to environment
  • 1644b1fc add pptx report
  • 1ab93aff (broken) start plotting
  • 094530f0 swithc sc2rf to a postprocess script
  • 02193d6e try generalizing sc2rf post-processing

v0.2.0

Notes

Bugs

  1. Fix bug in sc2rf_recombinants regions/breakpoints logic.
  2. Fix bug in sc2rf where a sample has no definitive substitutions.

Params

  1. Allow --breakpoints 0-4, for XN. We'll determine the breakpoints in post-processing.

  2. Bump up the min_len of sc2rf_recombinants to 1000 bp.

  3. Add param mutation_threshold to sc2rf.

  4. Reduce default mutation_threshold to 0.25 to catch [Issue #591](cov-lineages/pango-designation#591_.

  5. Bump up subtree size from 100 sequences to 500 sequences.

    • Trying to future proof against XE growth (200+ sequences)

  6. Discovered that --primers interferes with breakpoint detection, use only for debugging.

  7. Only use --enable-deletions in sc2rf for debug mode. Otherwise it changes breakpoints.

  8. Only use --private-mutations to sc2rf for debug mode. Unreadable output for bulk sample processing.

Report

  1. Change sc2rf_lineage column to use NA for no lineage found.

    • This is to troubleshot when only one breakpoint matches a lineage.

  2. Add sc2rf_mutations_version to summary based on a datestamp of virus_properties.json.

  3. Allow multiple issues in report.

  4. Use three status categories of recombinants:

    • Designated
    • Proposed
    • Unpublished

  5. Add column status to recombinants.

  6. Add column usher_extra to usher_metadata for 2022-05-06 tree.

  7. Separate out columns lineage and issue in report.

  8. Add optional columns to report.

  9. Fixed growth calculations in report.

  10. Add a Definitions section to the markdown/pdf report.

  11. Use parent order for breakpoint matching, as we see same breakpoint different parents.

  12. Add the number of usher placements to the summary.

Output

  1. Set Auspice default coloring to lineage_usher where possible.

  2. Remove nwk output from usher and usher_subtrees:

    • Pull subtree sample names from json instead

  3. Output linelist.exclude.tsv of false-positive recombinants.

Programs

  1. Update nextclade_dataset to 2022-04-28.
  2. Add taxoniumtools and chronumental to environment.
  3. Separate nextclade clades and pango lineage allele frequences in sc2rf.
  4. Exclude BA.3, BA.4, and BA.5 for now, as their global prevalence is low and they are descendants of BA.2.

Profiles

  1. Add a tutorial profile.

    • (N=2) Designated Recombinants (pango-designation)
    • (N=2) Proposed Recombinants (issues, UCSC)
    • (N=2) Unpublished Recombinants

  2. Add XL to controls.

  3. Add XN to controls.

  4. Add XR to controls.

  5. Add XP to controls.

Workflow

  1. Split usher_subtree and usher_subtree_collapse into separate rules.

    • This speeds up testing for collapsing trees and styling the Auspice JSON.

  2. Force include Nextclade recombinants (auto-pass through sc2rf).

  3. Split usher and usher_stats into separate rules.

Pull Requests

  • pull/13 Three status categories: designated, proposed, unpublished

Commits

  • 10388a6e update docs for v0.2.0
  • 32b9e8ab separate usher and usher_stats rule and catch 3 or 4 col usher
  • 70da837c update github issues and breakpoints for 636 and 637
  • 9ed10f17 skip parsing github issues that don't have body
  • 216cb28e put the date in the usher data for tutorial
  • c95cca0e update usher v0.5.3
  • 98c91bee finish reporting cycle 2022-05-11
  • e4755f16 new sc2rf mutation data by clade
  • 4a501d56 separate omicron lineages from omicron clades
  • d6185aaf testing change to auto-pass nextclade recombinants
  • 2e02922f add XL XN XR XP to controls
  • e2c9675b add usher_extra and qc file to sc2rf recombinants
  • 941a64c5 update github issues
  • 943cde95 add usher placements to summary
  • 0d0ffbd4 combine show-private-mutations with ignore-shared
  • f1d7e6c1 update sc2rf after terminal bugfixes
  • 8f4fd95a add country England to geo res
  • efeeb6ca add mutation threshold param sep for sc2rf
  • 9c42bc6c limit table col width size in report
  • 7d746e3f fix growth calculation
  • 0dc7f464 identify sc2rf lineage by breakpoints and parents
  • 19fc3721 add parents to breakpoints and issues
  • 27bbff0a generate geo_resolutions from ncov defaults lat longs
  • 86aa78ba add map to auspice subtrees
  • 2499827e add taxoniumtools and chronumental to env
  • ec46a569 change tutorial seq names from underscores to dashes
  • 27170a0b fix issues line endings
  • e8eb1215 update nextclade dataset to 2022-04-28
  • 89335c3a (broken) updating columns in report
  • 67475ecc update sc2rf
  • 79b7b2b9 add tip to readme
  • 10df6a54 remove all sample extraction from usher
  • 2ffbcb61 switch sc2rf submodule to ktmeaton fork
  • e2adaabe disable snakemake report in pipeline ci
  • f12fef14 edit line linst preview instructions
  • d10eb730 add collection date to tutorial
  • d4e0aa86 very preliminary credits and tutorial
  • e9c41e6e change ci pipeline to tutorial build
  • 4de7370d add tutorial data
  • 8d8c88fc set min version for click to troubleshoot env creation
  • c7fb50a4 better issue reporting
  • b2699823 update sc2rf

v0.1.2

Notes

  1. Add lineage XM to controls.

    • There are now publicly available samples.

  2. Correct XF and XJ controls to match issues.

  3. Create a markdown report with program versions.

  4. Fix sc2rf_recombinants bug where samples with >2 breakpoints were being excluded.

  5. Summarize recombinants by parents and dates observed.

  6. Change report.tsv to linelist.tsv.

  7. Use date_to_decimal.py to create num_date for auspice subtrees.

  8. Add an --exclude-clades param to sc2rf_recombinants.py.

  9. Add param --ignore-shared-subs to sc2rf.

    • This makes regions detection more conservative.
    • The result is that regions/clade will be smaller and breakpoints larger.
    • These breakpoints more closely match pango-designation issues.

  10. Update breakpoints in controls metadata to reflect the output with --ignore-shared-subs.

  11. Bump up min_len for sc2rf_recombinants to 200 bp.

  12. Add column sc2rf_lineage to sc2rf_recombinants output.

    • Takes the form of X*, or proposed{issue} to follow UShER.

  13. Consolidate lineage assignments into a single column.

    • sc2rf takes priority if a single lineage is identified.
    • usher is next, to resolve ties or if sc2rf had no lineage.

  14. Slim down the conda environment and remove unnecessary programs.

    • augur
    • seaborn
    • snipit
    • bedtools
    • Comment out dev tools: git and pre-commit.

  15. Use github api to pull recombinant issues.

  16. Consolidate *to* files into resources/issues.tsv.

  17. Use the --clades param of sc2rf rather than using exclude_clades.

  18. Disabled --rebuild-examples in sc2rf because of requests error.

  19. Add column issue to recombinants.tsv.

  20. Get ncov-recombinant version using tag.

  21. Add documentation to the report.

    • What the sequences column format means: X (+X)
    • What the different lineage classifers.

Pull Requests

  • pull/10 Automated report generation and sc2rf lineage assignments

Commits

  • 941f0c08 update CHANGELOG
  • bce219b6 fix notes conflict
  • cdb3bc7f fix duplicate pr output in autologs
  • 0a8ffd84 update notes for v0.1.2
  • 0075209b add issue to recombinants report
  • 0fd8fea0 (broken) troubleshoot usher collapse json
  • b0ab72b9 update breakpoints
  • a3058c57 update sc2rf examples
  • b5f2a0f8 update and clean controls data
  • f69f254c add curated breakpoints to issues
  • 4e9d2dc9 add an issues script and resources file
  • 16059610 major environment reduction
  • 5ced9193 remove bedtools from env
  • 28777cb9 remove seaborn from env
  • 01f459c4 remove snipit from env
  • 7d6ef729 remove augur from env
  • 9a2e948d fix pandas warnings in report
  • 78daee55 remove script usher_plot as now we rely on auspice
  • a7bd52f1 remove script update_controls which is now done manually
  • 93a30200 consolidate lineage call in report
  • 5f3e3633 hardcode columns for report
  • 6333fde4 improve type catching in date_to_decimal
  • 557627a4 update controls breakpoints and add col sc2rf_lineage
  • 7e2ad531 add param --ignore-shared-subs to sc2rf
  • 519a9eea overhaul reporting workflow
  • 6fa674f2 update controls metadata and dev notes
  • 46155a84 add XM to controls
  • d2d4cd80 update notes for v0.1.2
  • 17ae6eeb add issue to recombinants report
  • 2ab8dd30 (broken) troubleshoot usher collapse json
  • e4fd3352 update breakpoints
  • c743ad3d update sc2rf examples
  • 62e1ffc1 update and clean controls data
  • 9c401a0c add curated breakpoints to issues
  • 7cf953ad add an issues script and resources file
  • fbf35e51 major environment reduction
  • 1b1f16e9 remove bedtools from env
  • 7b650279 remove seaborn from env
  • b32608e7 remove snipit from env
  • 9cab231e remove augur from env
  • a69836a8 fix pandas warnings in report
  • b3137ed3 remove script usher_plot as now we rely on auspice
  • 06fa080d remove script update_controls which is now done manually
  • e8d46a64 consolidate lineage call in report
  • ccfea688 hardcode columns for report
  • 5172755e improve type catching in date_to_decimal
  • 74f0e528 update controls breakpoints and add col sc2rf_lineage
  • d4664015 add param --ignore-shared-subs to sc2rf
  • 659d7f83 overhaul reporting workflow
  • e8e3444f update controls metadata and dev notes
  • 07a5ff52 add XM to controls

v0.1.1

Notes

  1. Add lineage XD to controls.

    • There are now publicly available samples.

  2. Add lineage XQ to controls.

    • Has only 1 diagnostic substitution: 2832.

  3. Add lineage XS to controls.

  4. Exclude lineage XR because it has no public genomes.

    • XR decends from XQ in the UShER tree.

  5. Test sc2rf dev to ignore clade regions that are ambiguous.

  6. Add column usher_pango_lineage_map that maps github issues to recombinant lineages.

  7. Add new rule report.

  8. Filter non-recombinants from sc2rf ansi output.

  9. Fix subtrees_collapse failing if only 1 tree specified

  10. Add new rule usher_metadata for merge metadata for subtrees.

Commits

  • b8f89d5e update docs for v0.1.1
  • 2b8772ab update autologs for pr date matching
  • f2a7547d add low_memory_mode for issue #9
  • 94fc9426 add log to report rule
  • 861ffb17 update usher output image
  • fdee0da6 add new rule usher_metadata
  • c5003453 add max parents param to sc2rf recombinants
  • 70cad049 add max ambig filter to defaults for sc2rf
  • b4cc40f4 add script to collapse usher metadata for auspice
  • 847c6d24 catch single trees in usher collapse
  • 636778e0 rename sc2rf txt output to ansi
  • bae50814 change final target to report
  • 9a830085 add new rule report
  • 601e1728 add XD to controls
  • baa1d64e relax sc2rf --unique from 2 to 1 for XQ
  • bffbb9ad add column sc2rf_clades_filter
  • 109ed5d2 test sc2rf dev to not report ambiguous regions
  • d9fdffef fix tab spaces at end of usher placement
  • 085e1764 update sc2rf for tsv/csv PR
  • d2363855 set threads and cpus to 1 for all single-thread rules
  • 13027205 impose wildcard constraint on nextclade_dataset
  • 30e1406b fix typo in csv path for sc2rf
  • d6d8377a add XS breakpoints to metadata
  • 371e4069 add XS and XQ to controls
  • 1e31e429 add breakpoints reference file in controls
  • 3088ad60 catch if sc2rf has no output
  • 64211360 catch all extra args in slurm
  • c7a6b9ce remove unused nextclade_recombinants script
  • 38645ce9 remove codecov badge
  • 50fa9d89 update CHANGELOG for v0.1.0

v0.1.0

Notes

  1. Add Stage 1: Nextclade.

  2. Add Stage 2: sc2rf.

  3. Add Stage 3: UShER.

  4. Add Stage 4: Summary.

  5. Add Continuous Integration workflows: lint, test, pipeline, and release.

  6. New representative controls dataset:

    • Exclude XA because this is an Alpha recombinant (poor lineage accuracy).
    • Exclude XB because of current issue
    • Exclude XC because this is an Alpha recombinant (poor lineage accuracy).
    • Exclude XD because there are no public genomes.
    • Exclude XK because there are no public genomes.

Pull Requests

  • pull/3 Add Continuous Integration workflows: lint, test, pipeline, and release.

Commits