2.0.1

[evanroyrees]

What's Changed

• Environment and directory structure updates by @WiscEvan in Environment and directory structure updates #8
• resolved Dev branch lacks copyright notices, author attributions and distribution license #10 Contributors added and copyright year updated to 2020. by @WiscEvan in resolved #10 Contributors added and copyright year updated to 2020. #15
• Resolving issues [Dev branch] Issues with autometa/common/external/prodigal.py #16, [Dev branch] Issues with autometa/common/kmers.py #17, [Dev branch] Issues with autometa/common/external/bedtools.py #18, [Dev branch] Issues with autometa/common/coverage.py #21 and update to Autometa API and Logger by @WiscEvan in Resolving issues #16, #17, #18, #21 and update to Autometa API and Logger #25
• Resolved [Dev branch] Issues with autometa/common/external/samtools.py #19 added docstring, fixed nproc and removed depth function by @Sidduppal in Resolved #19 added docstring, fixed nproc and removed depth function #29
• Documentation by @Sidduppal in Documentation #34
• Issue create autometa conda recipe #5 Working conda recipe by @WiscEvan in Issue #5 Working conda recipe #38
• 🐛found in coverage by @WiscEvan in 🐛found in coverage #49
• fixes python2.7 BH-SNE #2 by @WiscEvan in fixes #2  #47
• Contributing Guidelines by @WiscEvan in Contributing Guidelines #50
• Add Markers class documentation. by @WiscEvan in Add Markers class documentation. #62
• Add main.py documentation (fixes [dev branch] Issues with autometa/__main__.py #60) by @WiscEvan in Add __main__.py documentation (fixes #60) #63
• Add functionality to bin without taxonomy. Update docstrings by @WiscEvan in Add functionality to bin without taxonomy. Update docstrings #65
• Documentation by @Sidduppal in Documentation #45
• Remove merge conflict resolution lines (Fixes Lines within markers.py from merge conflict resolution #68) by @WiscEvan in Remove merge conflict resolution lines (Fixes #68) #69
• 🎨🐛 Add mock import of modules and link to contribution guidelines (fixes [Dev branch] Document update needed #22) by @Sidduppal in 🎨🐛 Add mock import of modules and link to contribution guidelines (fixes #22) #70
• Resolves [dev branch] Issues with autometa/config/environ.py #55 Environ by @Sidduppal in Resolves #55 Environ #76
• fixes-[dev branch] Issues with autometa/common/metagenome.py #54 Metagenome by @WiscEvan in fixes-#54 Metagenome #66
• Update MAG class to MetaBin by @WiscEvan in Update MAG class to MetaBin #67
• hmmer by @Sidduppal in hmmer #72
• LCA by @WiscEvan in LCA #78
• Fix writing by @WiscEvan in Fix writing #82
• Update majority_vote by @WiscEvan in Update majority_vote #81
• pre-commit hooks by @WiscEvan in pre-commit hooks #92
• verbose bug by @WiscEvan in verbose bug #90
• Recursive DBSCAN by @WiscEvan in Recursive DBSCAN #84
• databases and utilities by @WiscEvan in databases and utilities #77
• Rank-specific binning by @WiscEvan in Rank-specific binning #96
• diamond.py by @Sidduppal in diamond.py #87
• Add support request issue template. by @WiscEvan in Add support request issue template. #97
• ncbi.py by @Sidduppal in ncbi.py #83
• Samtools by @Sidduppal in Samtools #103
• Binning stats/taxonomy summary by @WiscEvan in Binning stats/taxonomy summary #99
• decision tree classifier by @WiscEvan in decision tree classifier #100
• Fix config and setup of user project by @WiscEvan in Fix config and setup of user project #104
• Update project docstrings by @WiscEvan in Update project docstrings #108
• CI/CD by @WiscEvan in CI/CD #101
• 🐛 Change > to >= when calculating N50 by @chasemc in 🐛 Change > to >= when calculating N50 #119
• Fix Dockerfile by @WiscEvan in Fix Dockerfile #123
• Add support for gzipped assemblies by @WiscEvan in Add support for gzipped assemblies #129
• Update bug report template by @WiscEvan in Update bug report template #130
• Remove --multiprocess from autometa-kmers entrypoint by @WiscEvan in Remove --multiprocess from autometa-kmers entrypoint #127
• Add GC content std.dev. limit and coverage std. dev. limit Binning metrics by @WiscEvan in Add GC content std.dev. limit and coverage std. dev. limit Binning metrics #120
• Nextflow implementation template by @WiscEvan in Nextflow implementation template #118
• Update documentation by @Sidduppal in Update documentation #121
• Add feature to download google drive datasets by @ajlail98 in Add feature to download google drive datasets #138
• Add densmap embed method and fix binning-summary cluster column bug by @WiscEvan in Add densmap embed method and fix binning-summary cluster column bug #176
• Classification and Clustering Benchmarking by @WiscEvan in Classification and Clustering Benchmarking #141
• Nfcore and structuring modules for collaboration by @chasemc in Nfcore and structuring modules for collaboration #157
• Delete .gitattribute - there is a .gitattributes by @chasemc in Delete .gitattribute - there is a .gitattributes #190
• 🔥🍏 Remove duplicate standard slurm profiles by @WiscEvan in 🔥🍏 Remove duplicate standard slurm profiles #195
• Fix import error in databases.py by @WiscEvan in Fix import error in databases.py #194
• Fix/Create mock data subworkflow by @chasemc in Fix/Create mock data subworkflow #206
• 🐳:bug: Docker fix :whale: by @WiscEvan in 🐳:bug: Docker fix :whale: #213
• 📝 Update Documentation by @WiscEvan in 📝 Update Documentation #212
• 🎨 Add typehints and update kmers docstring by @WiscEvan in 🎨 Add typehints and update kmers docstring #208
• 🎨🐍 Add specific parsers for domtblout and tblout for hmmscan output formats by @WiscEvan in 🎨🐍 Add specific parsers for domtblout and tblout for hmmscan output formats #201
• 🐍🎨🐛 Update metagenome.length_filter(...) by @WiscEvan in 🐍🎨🐛 Update metagenome.length_filter(...) #210
• Fix bedtools genomecov deprecation (coverage calculation) by @WiscEvan in Fix bedtools genomecov deprecation (coverage calculation) #209
• 🎨🐚 Add bash-implementations of Autometa workflows by @WiscEvan in 🎨🐚 Add bash-implementations of Autometa workflows #202
• Nextflow documentation by @chasemc in Nextflow documentation #184
• 🔥📝 Reformat benchmarking docs by @WiscEvan in 🔥📝 Reformat benchmarking docs #215
• Refactor autometa-taxonomy-lca by @WiscEvan in Refactor autometa-taxonomy-lca #211
• 🎨🐳 Replace jason-c-kwan with jasonkwan for docker images by @WiscEvan in 🎨🐳 Replace jason-c-kwan with jasonkwan for docker images #217
• Update mock_data_reporter.Dockerfile by @chasemc in Update mock_data_reporter.Dockerfile #220
• 🐳💚📝 Add docker CI and update links by @WiscEvan in 🐳💚📝 Add docker CI and update links #216
• Simplify Licensing by @chasemc in Simplify Licensing #222
• Add check for nr.dmnd and nr.gz by @chasemc in Add check for nr.dmnd and nr.gz #221
• 🍏 Change Nextflow I/O behavior by @WiscEvan in 🍏 Change Nextflow I/O behavior #218
• 🍏🎨 add/update coverage handling by @WiscEvan in 🍏🎨 add/update coverage handling #223
• 🐍🐎 Large data mode by @WiscEvan in 🐍🐎 Large data mode #207
• Merge main into dev by @WiscEvan in Merge main into dev #224
• pytest & codecov CI by @WiscEvan in pytest & codecov CI #227
• Refactor samplesheet by @WiscEvan in Refactor samplesheet #228
• 🐛 🎨 🍏 Fix kingdom-handling and mounting NCBI databases into docker container by @WiscEvan in 🐛 🎨 🍏 Fix kingdom-handling and mounting NCBI databases into docker container #229
• Add error handling strategies for nextflow processes by @WiscEvan in Add error handling strategies for nextflow processes #231
• Release 2.0.0 by @WiscEvan in Release 2.0.0 #233
• 📝🎨⬆️🔥 update build files and respective docs by @WiscEvan in 📝🎨⬆️🔥 update build files and respective docs #234
• Add badges and links to README.md by @WiscEvan in Add badges and links to README.md #235
• GH action: Add dynamic docker tags by @WiscEvan in GH action: Add dynamic docker tags #236
• Update nextflow-workflow.rst by @samche42 in Update nextflow-workflow.rst #238
• 🐛🔥 Fix bedtools coverage calculation bug by @WiscEvan in 🐛🔥 Fix bedtools coverage calculation bug #243

New Contributors

• @chasemc made their first contribution in 🐛 Change > to >= when calculating N50 #119
• @samche42 made their first contribution in Update nextflow-workflow.rst #238

Full Changelog: 1.0.3...2.0.1

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This discussion was created from the release 2.0.1.