Release v0.3.0

v0.3.0

Notes

1. Manuscript submission.
2. New plotting of archaeological metadata.
3. Improved parsing of BEAST trees.

Commits

• 3b8f53b3 update notes and changelog for v0.3.0
• 9a88f562 Remove lsd2 from install workflow
• 68d59861 checkpoint denmark metadata
• cce4a39e Remove plotting SNPs from default targets to test CI
• 409d678a new denmark and plague notebook changes
• 342170b5 new timeline for individuals
• ad3d996a more geographic stats
• e2f9e68b new geo stats
• ef9006fd automated updated
• 789bb0c5 prettier beast estimates file
• 04387e4c time dependency and tree rates update
• 13f81fdc new script newick to nextstrain
• 07aa3807 automated update
• f532276a use old 2.MED tree
• 6f764559 update branch lengths notebooks
• 77aaca79 update notebooks for mean rate
• e276513b new plotting for mean rate
• 4553d334 locus cov changes for main
• 78a1bc7a initialize bash shell for conda activate
• 11e26976 add lsd2 to dockerfile
• See CHANGELOG.md for additional commits.

Release v0.2.8

v0.2.8

Notes

1. Add Jupyter Notebook for processing BEAST output.
2. Updates to Root-To-Tip Regression and Geographic.
3. Update and sync all metadata files.
4. Separated auspice output into beast/ml datasets.
5. Add beast timetrees to auspice.

Commits

• 25acf3d7 update CHANGELOG for v0.2.8
• 64df6aac stable notebooks and update docs
• ba6a6c66 remove screenshot
• 7c5b5cd9 update autologs
• b874f75b checkpoint notebooks before troubleshooting
• acd301df rearrange confidence intervals
• 5302b404 first draft of beast trees
• bb617a82 checkpoint beast
• 4153f6e8 add legends and white background
• c3f22efb correct rtt p_values for multiple tests
• faafa254 add mantel test to iqtree stats
• fc321f4c update auspice time-dependency
• 49314a4e add time-dependency to auspice
• 14796fe6 update iqtree stats
• c94afdce plotting overhaul
• a7b01119 add joint probability of mugration and branch support
• 0fc3a25f update iqtree stats with ibd
• 87c715f1 update plot target and load beast dir

Release v0.2.7

v0.2.7

Notes

1. Add mugration to workflow.
2. Upgrade auspice to 2.25.1
3. Remove old Jupyter Notebooks
4. Curate host metadata.
5. Consolidate visualization to auspice notebook.

Pull Requests

• pull/7

Commits

• 6e469bc6 update docs for v0.2.7
• 120aa0a0 Merge pull request #7 from ktmeaton/dev
• f0a2d742 update docs
• faa9731e update database
• 65e5dd89 add host as visualization variable
• d6803fbd add plotting map
• 4e0f6de1 add boxplots for rate and tmrca
• 6b039800 fix 0.PE subclades and add blank label
• 51a98838 start experimenting with p-values
• f199b8bb update auspice metadata
• 8ded9416 remove mugration from all targets
• 821de4d4 add temporal constraint plotting and input to tsv
• 4f8eb7b6 reset test outgroup to reference
• c20f5580 start writing bootstrap function
• 7ed6eb6f test linear regression in stats
• 70f780ba remove old jupyter notebooks
• a1034200 add auspice to snakemake
• 9dc376ad add prune target for mugration
• ca46113f create auspice by subtree
• fcfa1dd9 fix reference date in metadata
• See CHANGELOG.md for additional commits.

v0.2.6

v0.2.6

Notes

1. Put project specific results in seperate repository.
2. Added 2020 Latvia samples to database, mark as low coverage for now.
3. Move log directory to within results.
4. Remove xml tree output from notebooks.
5. Create scripts to backup, restore, and clean projects.
6. Remove plot_table rules and script.
7. Only include visual files into the report.
8. Put config files inside the associated project directory.
9. Update function identify_local_sample to use database.
10. Environment addition: augur, cartopy, ffpmeg, snp-dists, bokeh.
11. Create Pairwise SNP matrix.
12. Remove results folder from docs.
13. Create new output folder collect for detect snp density.
14. Remove US Kim strain, mark as laboratory manipulation.
15. Clean snp density files from version control.
16. Add country to continent mapping for metadata.
17. Improvements to plotting missing data and filtering log.
18. Change all metadata column names to lowercase.
19. Changed from TreeTime to LSD2.
20. Included rules to prepare for BEAST.
21. Jupyter Notebooks pertaining to TreeTime are not used.

Commits

• 3b93d735 update notes for v0.2.6
• 47d7feff Merge pull request #6 from ktmeaton/dev
• 4e43f4f6 update docs notes
• b24b1d97 create newick and nexus trees for beast
• c3097266 fix branch lengths in conversion scripts
• 8fba8a68 add more date col to metadata
• 2d5b7545 fix bug in filter_sites
• 5dd79f8f fix typo in metadata script
• 2169f03a add new rule to filter outgroup from iqtree
• f36ae76e fix typo in eager_tsv script
• 62c1c5cf remove eager log from output and command
• 3790bdd1 first attempt at fixing eager CI
• 3acb65fb restore eager log and fix typo
• cfbc4698 Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
• cd24348d extract and plot subtree
• cd6f133f catch constant sites in filter script
• 035c9292 renable eager log
• bb0f9ceb first round of plot phylo with compatability for spread3
• 4623efb0 extra params for lsd2
• 35ce0447 mega plotting update
• See CHANGELOG.md for additional commits.

Release v0.2.5

v0.2.5

Notes

1. Separate mugration notebook into model and plot.
2. Add a heatmap test, output to misc.
3. Create a new rule to generate locus coverage.
4. Remove output directory of eager rule.
5. Make a list of target genes
6. Hard code target genes into ref locus bed
7. Move ref locus bed to reference
8. Create gene by gene coverage.
9. Analyze both coverage and depth of loci.
10. Compare gene to plasmid coverage (pla, pPCP1)
11. Apply a coverage filter for pPCP1 plasmid.
12. Add locus coverage info to nexus tree.
13. Created spreadmaps for branch major.

Pull Requests

• pull/4 v0.2.5

Commits

• 596d55c finish notes for v0.2.5
• 3b34108 add spreadmaps for branch major
• abb53af geo spreadmap for branch major
• 858b1f9 first geo attempt spreadmap for branch number
• 5e1ba24 update markdownlint workflow
• 3f397c8 add cartopy to env
• 9c86378 apply a coverage filter for pPCP1
• 8ad86bb add gene to plasmid depth comparison
• 01ecfc0 update locus coverage with depth
• c8bbf55 remove premature exit in locus coverage script
• 818d701 run cov and depth on locus coverage
• 6868691 make locus coverage it's own notebook
• 050dbb4 locus coverage including pla
• 1bc297b add execute permissions to locus bed
• 9efb53a separate rules locus_bed and locus_coverage
• dd3c506 Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
• df071bf add custom genes to locus coverage
• c3b28e6 Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
• 75fbf80 add locus coverage results
• cd56bf5 remove output dir from eager rule
• See CHANGELOG.md for additional commits.

v0.2.4 - Mugration Integration

v0.2.4

Notes

1. Update coord_x and coord_y in clock_model.
2. Save timetrees and divtrees for all relevant methods.
3. Mugration working for all attributes individually.
4. Changed mugration to work with timetree object input.
5. Start version tagging auspice visualizations.

Commits

• 58dd2e1 update notes, changelog, and auspice json for v0.2.4
• 46d3d1f fixed mugration by making sure to copy tree div
• e886d00 working mugration for Country
• 1cdf425 working mugration for Branch_Number
• 7ea625a save timetrees and divtrees for all relevant methods
• 0723ae4 update coord_x and coord_y in clock_model
• 3d7890e prepare notes for development post-v0.2.3
• 4dee9cd update CHANGELOG for v0.2.3

Nextstrain Exhibit v0.2.4

v0.2.3 - Timetree Marginal Parameters

v0.2.3

Notes

1. Experiment with relaxed clock parameters.
2. Experiment with marginal likelihood parameters.
3. Experiment with the coalescent parameters.
4. Catch bad lower confidence bounds.
5. Think about snippy_dir in rule eager...

Pull Requests

• pull/3 v0.2.3

Commits

• 51adae7 update notes for v0.2.3
• fc418ff Merge pull request #3 from ktmeaton/dev
• 0f8f57d excellent timetree marginal parameters
• 181f944 add comments to nexus for clock_model
• 18a7b0e checkpoint with working but unstable marginal estimate
• ab3f911 add comments to nexus for parse_tree
• c33bd64 slack:0.1, blm: joint, tc:def, time_marginal:def
• b34519f slack:0.5, blm: joint, tc:def, time_marginal:def
• 4158f9a first pass at timetree marginal parameters
• 1bd0899 Merge pull request #2 from ktmeaton/dev

v0.2.2 - Timetree Joint Parameters

v0.2.2

Notes

1. Add entropy to augur.
2. Add mugration models to augur.
3. Add clock model to augur.
4. Add clock lengths to augur.
5. Add date confidence to augur.
6. Scatterplot of taxa vs rtl for treemmer.
7. Prune tree, dataframe, and alignment with treemmer.
8. Confirm pruning consistency between tree, dataframe, and alignment (n=247).
9. Plot tree comparison.
10. Checkpoint before clock modelling in BEAST.
11. Use pickle to save objects of Jupyter notebooks.
12. New jupyter notebooks for post-phylo.
13. Put jupyter notebook output into results.
14. Think about snippy_dir in rule eager...

Pull Requests

• pull/2 v0.2.2

Commits

• be38c62 use release workflow from autologs
• e5022e1 start testing marginal parameters
• c416a43 rename dev notes to v0.2.2
• bf00b71 rerun clock model with good joint param
• 6c1d044 rerun clock model with terrible param
• 8cdab57 put jupyter notebook output into results
• e5a74e2 remove old docs parse_tree folder
• 1ca7bee reorder jupyter notebooks
• 0b2c710 checkpoint before notebook overhaul
• 541b953 write tree and df objects with dill for parse_tree
• 6a6ccdd add dill to environment
• 77e2b72 add autologs as submodule
• 0365b53 add last timetree model updates
• d211d7f Merge branch 'dev' of https://github.com/ktmeaton/plague-phylogeography into dev
• ff365f7 Merge branch 'master' into dev
• ea998f2 Merge branch 'master' of https://github.com/ktmeaton/plague-phylogeography
• 51a4e94 checkpoint before using marginal years function
• 40b291a update docs for v0.2.2
• ff71d89 checkpoint before clock modelling in BEAST
• 1471e40 plot tree comparison
• See CHANGELOG.md for additional commits.

v0.2.1 - Automate Changelog

Release v0.2.1

Notes

1. Automate commit history.
2. Automate release notes.
3. Automate CHANGELOG updates.

Commits

• f30964b disable singularity from install testing
• 4aa4cdc release log has truncated commits and changelog has full
• d039c74 automatically create changelog
• 36b672f don't run full CI on ver tags
• 6d72628 refine CI workflows to pushes on master or dev
• 46e443f fix dockerfile path for release
• 6aaaa5e automate release on ver tags
• ec5504a automate commit notes
• 023214c update notes for v0.2.1
• 35ab58c provide config file for flake8 in lint CI
• 8857dcc add treemmer notebook results
• f862d44 disable singularity from CI
• d136168 add treemmer and ete3 to env
• 05aa4ce update workflow for multiqc eager dir
• 59e94d4 update augur and auspice export for confidence
• 9d73947 separate the augur and auspice json
• 730002b update branch_support notebook and output
• 419cbdb update parse_tree notebook and output
• fa522bb auto publish auspice files and use clock filter in parse_tree
• ceffb5f split timetree into model and plot

v0.2.0 - Snakemake

• Convert pipeline from Nextflow to Snakemake
• Containerize with conda, singularity, and docker.
• Stabilize nf-core/eager to 2.2.1.
• Add jupyter notebooks