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Autometa
Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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Release 2.0.3
#259
evanroyrees
closed
2 years ago
1
Check NCBI connection instead of pinging google DNS
#258
ajlail98
closed
2 years ago
2
internet_is_connected() function
#257
paulineauffret
closed
2 years ago
4
:art::bug::snake: Fix `autometa-length-filter` bug when `--output-fasta` is specified without an output directory
#256
evanroyrees
closed
2 years ago
2
:bug:🪲 Prevent edge case where MAG completeness is incorrectly computed
#255
evanroyrees
opened
2 years ago
0
:art::bug::snake: Convert 'unclassified' taxids of 0 to root taxid of 1
#254
evanroyrees
closed
2 years ago
9
:green_apple::snake::art: add exit status code of 204 for raised BinningError
#253
evanroyrees
closed
2 years ago
2
:art::fire::green_apple: Replace incorrect runtime defaults
#252
evanroyrees
closed
2 years ago
1
🔥🍏 Remove duplicate nextflow runtime defaults
#251
evanroyrees
closed
2 years ago
0
allow utf-8-sig sample sheet files
#250
chasemc
closed
2 years ago
2
in check_samplesheet.py, incorporate more flexible encoding when reading
#249
shaneroesemann
closed
2 years ago
0
Add CITATION file (#242)
#248
evanroyrees
closed
2 years ago
2
:bug: Fix the NoneType error during initating the LCA object (#246)
#247
chtsai0105
closed
2 years ago
2
autometa-taxonomy-lca return TypeError without specifying --cache
#246
chtsai0105
closed
2 years ago
3
README should have link to contribution guidelines in the documentation
#245
jason-c-kwan
closed
2 years ago
0
:bug::fire: Fix bedtools coverage calculation bug
#243
evanroyrees
closed
2 years ago
1
Add CITATION file
#242
shaneroesemann
closed
2 years ago
7
You can add a CITATION file to your repository to help users correctly cite your software.
#241
chasemc
closed
2 years ago
0
Migrate documentation from reStructuredText to MyST Markdown
#240
evanroyrees
opened
2 years ago
4
Calculation of coverage
#239
chtsai0105
closed
2 years ago
1
Update nextflow-workflow.rst
#238
samche42
closed
2 years ago
2
No markers found - attempts made to find/count kmers
#237
samche42
closed
2 years ago
2
GH action: Add dynamic docker tags
#236
evanroyrees
closed
2 years ago
2
Add badges and links to README.md
#235
evanroyrees
closed
2 years ago
1
:memo::art::arrow_up::fire: update build files and respective docs
#234
evanroyrees
closed
2 years ago
2
Release 2.0.0
#233
evanroyrees
closed
2 years ago
1
Add error handling strategies for nextflow processes
#231
evanroyrees
closed
2 years ago
1
🍏 Add fail safe for `--resume` flag
#230
evanroyrees
closed
2 years ago
1
🐛 🎨 🍏 Fix kingdom-handling and mounting NCBI databases into docker container
#229
evanroyrees
closed
2 years ago
1
Refactor samplesheet
#228
evanroyrees
closed
2 years ago
1
pytest & codecov CI
#227
evanroyrees
closed
2 years ago
1
Notes on how to upgrade to current nf-core standards
#226
chasemc
opened
2 years ago
1
release 2.0
#225
evanroyrees
closed
2 years ago
4
Merge main into dev
#224
evanroyrees
closed
2 years ago
0
:green_apple::art: add/update coverage handling
#223
evanroyrees
closed
2 years ago
1
Simplify Licensing
#222
chasemc
closed
2 years ago
1
Add check for nr.dmnd and nr.gz
#221
chasemc
closed
2 years ago
0
Update mock_data_reporter.Dockerfile
#220
chasemc
closed
2 years ago
1
Add helpful error message for missing module docker image
#219
chasemc
closed
2 years ago
2
🍏 Change Nextflow I/O behavior
#218
evanroyrees
closed
2 years ago
10
:art::whale: Replace jason-c-kwan with jasonkwan for docker images
#217
evanroyrees
closed
2 years ago
0
:whale::green_heart::memo: Add docker CI and update links
#216
evanroyrees
closed
2 years ago
1
:fire::memo: Reformat benchmarking docs
#215
evanroyrees
closed
2 years ago
0
Add Jupyter notebook examples / autometa code snippets
#214
evanroyrees
opened
2 years ago
0
🐳:bug: Docker fix :whale:
#213
evanroyrees
closed
2 years ago
0
:memo: Update Documentation
#212
evanroyrees
closed
2 years ago
4
Refactor autometa-taxonomy-lca
#211
evanroyrees
closed
2 years ago
0
:snake::art::bug: Update metagenome.length_filter(...)
#210
evanroyrees
closed
2 years ago
0
Fix bedtools genomecov deprecation (coverage calculation)
#209
evanroyrees
closed
2 years ago
0
:art: Add typehints and update kmers docstring
#208
evanroyrees
closed
2 years ago
0
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