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Autometa: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[2.1.0] - 2022-05-11

Added

  • Addition of autometa entrypoint to retrieve info on citation, version and other commands
  • 🍏 Addition of autometa version written within each autometa-related nextflow process
  • 🐚 The autometa version is emitted at the beginning of the autometa bash workflow.

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

Dependencies

  • 🎨 Pinned black version to 22.3.0
  • ⬆️:green_heart: upgrade diamond to version 2.0.14

[2.0.3] - 2022-04-07

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: https://github.com/KwanLab/Autometa/compare/2.0.2...2.0.3

[2.0.2] - 2022-03-15

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: https://github.com/KwanLab/Autometa/compare/2.0.1...2.0.2

[2.0.1] - 2022-02-24

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 @Sidduppal 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: https://github.com/KwanLab/Autometa/compare/1.0.3...2.0.1

[2.0.0] - 2022-02-09

Second release of Autometa

Added

  • 🍏 Created autometa nextflow workflow with the nf-core template.
  • 🐚 Created autometa bash workflow
  • Refactored entire codebase for easy installation using pip and/or bioconda
  • Addition of various k-mer embedding parameters:
    • k-mer size
    • normalization method
    • PCA dimensions
    • embedding method
  • Addition of HDBSCAN clustering method
  • Addition of autometa entrypoints
  • Easy install with make commands in Makefile
  • Easy installation using pip
  • Easy installation using conda install -c bioconda autometa
  • Autometa library of functions available within the python environment
  • Granularity between autometa tasks to reduce re-computations on failed tasks
  • Configuration to specify paths to required databases
  • Added tests for CI/CD
  • 🐳 Update Dockerfile to conform to new autometa environment & commands
  • 📝 Addition of documentation hosted on autometa.readthedocs.io
  • Dependencies specified in autometa-env.yml
  • Dependencies specified in requirements.txt

Fixed

  • 🎨🐍 Restructured source code directory to allow installation of autometa console scripts
  • 🎨🐍 Restructured source code scripts to prevent calling code on import

Removed

  • python 2.7
  • All autometa version 1.* commands