Release 2.2.0

@chasemc

Fix "TypeError: boolean value of NA is ambiguous" Issue #360 in #361 by @chasemc and @Sidduppal

Full Changelog: 2.2.2...2.2.3

@chasemc

What's Changed

⬆️ bump readthedocs-sphinx-search; 0.1.1 to 0.3.2 by @chasemc in #354
🐛 Fixes Biopython deprecation warning by @Sidduppal in #350
Fix "ncbi rsync error when downloading markers" #347 in #352 by @Sidduppal
⬆️ Pin BioPython to >=1.82
⬆️ Pin Pandas to >=1.5
Release 2.2.2 by @Sidduppal in #359

Full Changelog: 2.2.1...2.2.2

@Sidduppal

What's Changed

🧑‍🔧 📝 Fix docs by @Sidduppal in #323
Step by step walkthrough by @kaw97 in #314
🎨 🍏 Issue 330 redo by @shaneroesemann in #338
🔥🐳💚 Fix docker-builds by removing pinned dependencies by @WiscEvan in #340
singularity image urls by @kaw97 in #316
helpful error message added by @RajnishProgrammer in #307
💚:bug::snake: Fix bug for 0 passing predictions by @WiscEvan in #341
🐛 Fix GTDB database setup by @Sidduppal in #329
🐛🐚 Fix GTDB taxon-binning workflow by @shaneroesemann in #339
📝 Update documentation by @WiscEvan in #342
🐍🎨🔥🐛 Fix UnboundLocalError bug by @WiscEvan in #325
🐛🎨🐍 Refactor 'unclassified' handling by @kaw97 and @WiscEvan in #343
Release 2.2.1 by @WiscEvan in #344

New Contributors

@RajnishProgrammer made their first contribution in #307

Full Changelog: 2.2.0...2.2.1

@jason-c-kwan

Release 2.2.0

Breaking changes 💣 💔🙈

Autometa's autometa-taxonomy and autometa-binning-summary entrypoints (instead of taking --ncbi as an input parameter) now take --dbdir and --dbtype to allow the user to use either the NCBI or GTDB database.

Command	💔 Previous 💔	💚 New 💚
`autometa-taxonomy`	`--ncbi`	`--dbdir <ncbi-database-dirpath>`, `--dbtype ncbi` (choices: ncbi, gtdb)
`autometa-binning-summary`	`--ncbi`	`--dbdir <ncbi-database-dirpath>`, `--dbtype ncbi` (choices: ncbi, gtdb)

NOTE: For implementation details for integrating other taxonomy databases see #284

🐚 Additional autometa workflows

Addition of workflow where only required inputs are reads and assembly
autometa.sh and autometa-large-data-mode.sh now require taxa_routine as an input parameter (choices are "ncbi" or "ncbi_gtdb". Autometa workflow now contains an optional sub-workflow where binning is guided by GTDB taxonomy after retrieving bacteria and archaea classified using the NCBI database.

TaxonomyDatabase

🐍 GTDB taxonomy integration to use within Autometa's taxon-binning and genome-binning workflows.

For more information on GTDB database setup see the Autometa GTDB database documentation

(autometa) evan@userserver:~/Autometa$ autometa-setup-gtdb -h
usage: autometa-setup-gtdb [-h] --reps-faa REPS_FAA --dbdir DBDIR [--cpus CPUS]

optional arguments:
  -h, --help           show this help message and exit
  --reps-faa REPS_FAA  Path to directory containing GTDB ref genome animo acid data sequences. Can be tarballed.
  --dbdir DBDIR        Path to output GTDB database directory
  --cpus CPUS          Number of cpus to use for diamond-formatting GTDB database

TL;DR

Abstraction of taxonomy databases using TaxonomyDatabase abstract base class with required abstractmethods.

This is currently implemented for both the NCBI and GTDB taxonomy database. Future taxonomy database integrations should follow the format from the TaxonomyDatabase class.

CAMI formatter

Binning validation/benchmarking utilities added/updated such as formatting autometa binning results into biobox format

Misc

💚 Fix pytest requirements in GH actions
🐛⬇️ pin scipy and joblib to avoid hdbscan import error
🐍🤫 Fix deprecated pandas method invocation in bedtools.py

What's Changed

📝 Added contribution documentation by @jason-c-kwan in #277
🎨🐍 Add CAMI formatter entrypoint autometa-cami-format by @WiscEvan in #276
🎨🐍 Update deprecated pandas method invocation by @WiscEvan in #279
⬇️ 💚 force scipy==1.8 by @kaw97 in #286
🐚 New bash files for Autometa workflow by @samche42 in #281
⬆️ 🎨 Allow the use of gtdb taxonomy in Autometa by @Sidduppal in #284
Add --average-method parameter to autometa-benchmark by @WiscEvan in #290
GTDB integration by @Sidduppal and @WiscEvan in #284

New Contributors

@jason-c-kwan made their first contribution in #277
@kaw97 made their first contribution in #286

Full Changelog: 2.1.0...2.2.0

@chasemc

[2.1.0] - 2022-05-12

`Added`

🐍autometa entrypoint to retrieve info on --citation, --version and no argument lists other autometa commands
🍏 The autometa version is written after completion of each autometa-related nextflow process
🐚 The autometa version is emitted at the beginning of the autometa bash workflow.
🐍 NCBI.py will now search delnodes.dmp for any taxids retrieved from blast output and convert to root (taxid=1)

`Fixed`

🐚🐛 Renamed incorrect variables $coverage to $coverages and $clustering_method to $cluster_method in workflows/autometa.sh
🐍🐛 Fix use of kwargs in kmers embed(..., *kwargs) function
🐍🐛 Fix passing n_jobs to kmers embed(..., n_jobs=1) function
🍏 🐳Add params.autometa_image_tag to mock_data_reporter process
🍏 🐳 Add params.autometa_image_tag to get_genomes_for_mock process

`Dependencies`

⬆️💚 Pinned black version to 22.3.0
⬆️:green_apple: upgrade diamond to version 2.0.14

`Removed`

🔥💚 Removed tests/requirements.txt and consolidated to tests/environment.yml

What's Changed (from the git logs)

🎨🐍 Add taxid conversion from 'unclassified' to 1 for taxon-profiling benchmarking by @WiscEvan in #260
📝 Update installation directions for bash workflow by @WiscEvan in #262
🐍🐛 Fix parsing taxids to delnodes set by @WiscEvan in #265
⬆️ 🍏 Upgrade Diamond 2.0.9 -> 2.0.14 by @chasemc in #264
🎨🐛🐍 Add n_jobs to embed(...) func. Replace **method_args w/ **method_kwargs by @WiscEvan in #267
Versioning by @WiscEvan in #269
🎨🍏 Add autometa --version to autometa nextflow files by @WiscEvan in #271
🐛🐚 Fix variable name for autometa-binning-summary by @WiscEvan in #272
Release 2.1.0 by @WiscEvan in #273

Full Changelog: 2.0.3...2.1.0

@shaneroesemann

What's Changed

📝 Add CITATION file by @shaneroesemann in #242
🐛🎨🍏 Allow utf-8-sig sample sheets #250
🐛📝🍏 Replace incorrect runtime defaults specified in nf-core launch command #252
🎨🍏 Continue nextflow workflow (without termination) if bins are not recovered from a particular dataset #253
🎨🐛 autometa-benchmark entrypoint, when checking taxid classifications, now converts any taxids of 0 to 1 #254
🐛 NCBI connection is checked prior to NCBI database files download rather than pinging google DNS #258
🐛 Fix autometa-length-filter bug where specifying a directory when writing to --output-fasta was required (now optional) #256
💚 ⬆️:whale::green_apple: Bump version to 2.0.3 in VERSION and manifest.version in nextflow.config s.t. autometa docker images used in nextflow workflow correspond to most recent release

New Contributors

@shaneroesemann made their first contribution in #242

Full Changelog: 2.0.2...2.0.3

@chtsai0105

What's Changed

🐛 Fix the NoneType error during initating the LCA object (#246) by @chtsai0105 in #247

New Contributors

@chtsai0105 made their first contribution in #247

Full Changelog: 2.0.1...2.0.2

@Sidduppa 8000 l

What's Changed

Environment and directory structure updates by @WiscEvan in #8
resolved #10 Contributors added and copyright year updated to 2020. by @WiscEvan in #15
Resolving issues #16, #17, #18, #21 and update to Autometa API and Logger by @WiscEvan in #25
Resolved #19 added docstring, fixed nproc and removed depth function by @Sidduppa 8000 l in #29
Documentation by @Sidduppal in #34
Issue #5 Working conda recipe by @WiscEvan in #38
🐛found in coverage by @WiscEvan in #49
fixes #2 by @WiscEvan in #47
Contributing Guidelines by @WiscEvan in #50
Add Markers class documentation. by @WiscEvan in #62
Add main.py documentation (fixes #60) by @WiscEvan in #63
Add functionality to bin without taxonomy. Update docstrings by @WiscEvan in #65
Documentation by @Sidduppal in #45
Remove merge conflict resolution lines (Fixes #68) by @WiscEvan in #69
🎨🐛 Add mock import of modules and link to contribution guidelines (fixes #22) by @Sidduppal in #70
Resolves #55 Environ by @Sidduppal in #76
fixes-#54 Metagenome by @WiscEvan in #66
Update MAG class to MetaBin by @WiscEvan in #67
hmmer by @Sidduppal in #72
LCA by @WiscEvan in #78
Fix writing by @WiscEvan in #82
Update majority_vote by @WiscEvan in #81
pre-commit hooks by @WiscEvan in #92
verbose bug by @WiscEvan in #90
Recursive DBSCAN by @WiscEvan in #84
databases and utilities by @WiscEvan in #77
Rank-specific binning by @WiscEvan in #96
diamond.py by @Sidduppal in #87
Add support request issue template. by @WiscEvan in #97
ncbi.py by @Sidduppal in #83
Samtools by @Sidduppal in #103
Binning stats/taxonomy summary by @WiscEvan in #99
decision tree classifier by @WiscEvan in #100
Fix config and setup of user project by @WiscEvan in #104
Update project docstrings by @WiscEvan in #108
CI/CD by @WiscEvan in #101
🐛 Change > to >= when calculating N50 by @chasemc in #119
Fix Dockerfile by @WiscEvan in #123
Add support for gzipped assemblies by @WiscEvan in #129
Update bug report template by @WiscEvan in #130
Remove --multiprocess from autometa-kmers entrypoint by @WiscEvan in #127
Add GC content std.dev. limit and coverage std. dev. limit Binning metrics by @WiscEvan in #120
Nextflow implementation template by @WiscEvan in #118
Update documentation by @Sidduppal in #121
Add feature to download google drive datasets by @ajlail98 in #138
Add densmap embed method and fix binning-summary cluster column bug by @WiscEvan in #176
Classification and Clustering Benchmarking by @WiscEvan in #141
Nfcore and structuring modules for collaboration by @chasemc in #157
Delete .gitattribute - there is a .gitattributes by @chasemc in #190
🔥🍏 Remove duplicate standard slurm profiles by @WiscEvan in #195
Fix import error in databases.py by @WiscEvan in #194
Fix/Create mock data subworkflow by @chasemc in #206
🐳:bug: Docker fix :whale: by @WiscEvan in #213
📝 Update Documentation by @WiscEvan in #212
🎨 Add typehints and update kmers docstring by @WiscEvan in #208
🎨🐍 Add specific parsers for domtblout and tblout for hmmscan output formats by @WiscEvan in #201
🐍🎨🐛 Update metagenome.length_filter(...) by @WiscEvan in #210
Fix bedtools genomecov deprecation (coverage calculation) by @WiscEvan in #209
🎨🐚 Add bash-implementations of Autometa workflows by @WiscEvan in #202
Nextflow documentation by @chasemc in #184
🔥📝 Reformat benchmarking docs by @WiscEvan in #215
Refactor autometa-taxonomy-lca by @WiscEvan in #211
🎨🐳 Replace jason-c-kwan with jasonkwan for docker images by @WiscEvan in #217
Update mock_data_reporter.Dockerfile by @chasemc in #220
🐳💚📝 Add docker CI and update links by @WiscEvan in #216
Simplify Licensing by @chasemc in #222
Add check for nr.dmnd and nr.gz by @chasemc in #221
🍏 Change Nextflow I/O behavior by @WiscEvan in #218
🍏🎨 add/update coverage handling by @WiscEvan in #223
🐍🐎 Large data mode by @WiscEvan in #207
Merge main into dev by @WiscEvan in #224
pytest & codecov CI by @WiscEvan in #227
Refactor samplesheet by @WiscEvan in #228
🐛 🎨 🍏 Fix kingdom-handling and mounting NCBI databases into docker container by @WiscEvan in #229
Add error handling strategies for nextflow processes by @WiscEvan in #231
Release 2.0.0 by @WiscEvan in #233
📝🎨⬆️🔥 update build files and respective docs by @WiscEvan in #234
Add badges and links to README.md by @WiscEvan in #235
GH action: Add dynamic docker tags by @WiscEvan in #236
Update nextflow-workflow.rst by @samche42 in #238
🐛🔥 Fix bedtools coverage calculation bug by @WiscEvan in #243

New Contributors

@chasemc made their first contribution in #119
@samche42 made their first contribution in #238

Full Changelog: 1.0.3...2.0.1

Full Changelog: 2.0...2.0.0

🐍 Deprecate python2.7 code
🐳 🐛 Dockerfile fix

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Release 2.2.0

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