biocore metagenomics_pooling_notebook issues

biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing

MIT License

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issues

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Short-term lane-setting solution possibility

#252 AmandaBirmingham closed 4 hours ago
1
Initial tellseq sample sheet support

#251 AmandaBirmingham closed 1 day ago
0
Meta T notebook updates fall24

#250 RodolfoSalido opened 4 days ago
0
Fix invalid notebook json left over from manual merge

#249 AmandaBirmingham closed 5 days ago
0
Multiproject plate support, updated blanks handling

#248 AmandaBirmingham closed 1 week ago
5
Ensure NPH_calc_df_SLURRY.ipynb always pulls the latest abs_quant_sample_info_calc.yml from github

#247 AmandaBirmingham opened 1 week ago
0
The final version!

#246 AmandaBirmingham closed 1 week ago
0
Added function to parse a sample-sheet into dataframes.

#245 charles-cowart closed 3 hours ago
5
Strip tubecode leading zeroes

#244 AmandaBirmingham closed 4 days ago
2
updated load_sample_sheet().

#243 charles-cowart closed 2 weeks ago
1
add support for pooling file generation from multiple library plates

#242 RodolfoSalido opened 1 month ago
2
add drop_zeros attribute to read_visionmate_file() to drop leading zeros.

#241 RodolfoSalido closed 4 days ago
4
Catch spaces in project name/abbreviation

#240 cbrenchy opened 1 month ago
5
Pin seqtk to v1.4 or above to fix spontaneous CI errors

#239 AmandaBirmingham closed 1 month ago
0
sample-sheets w/positive controls are fully descriptive

#238 charles-cowart opened 1 month ago
2
Possibly Merge v101 and v102 spreadsheets

#237 charles-cowart opened 2 months ago
0
Refactor use of `strict` parameter on `sample_sheet.make_sample_sheet()`

#236 AmandaBirmingham opened 2 months ago
1
Newer sample-sheet types may not need a remapper.

#235 charles-cowart opened 2 months ago
0
Centralize constants defining sequencers

#234 AmandaBirmingham opened 2 months ago
0
Refactor `sections` property of `KLSampleSheet` to reduce confusion with `_sections` property of parent class

#233 AmandaBirmingham opened 2 months ago
2
Multiproject plate: support for absquant

#232 AmandaBirmingham closed 2 months ago
1
Multiproject plate

#231 AmandaBirmingham closed 2 months ago
0
Multiproject plate: notebooks changes!

#230 AmandaBirmingham closed 2 months ago
0
Cleaned up test_data input and output for notebook templates

#229 RodolfoSalido closed 2 months ago
2
Bring master changes into multiproject plate

#228 AmandaBirmingham closed 3 months ago
0
Bring master changes into multiproject_plate branch

#227 AmandaBirmingham closed 3 months ago
0
Changes based on feedback

#226 charles-cowart opened 3 months ago
0
generate_override_cycles_value() added.

#225 charles-cowart closed 3 months ago
6
Hotfix incorrect variables in file checks, set katharoseq_dir to None ...

#224 AmandaBirmingham closed 3 months ago
1
Multiproject plate, part 2: constants and centralized sample sheet functionality

#223 AmandaBirmingham closed 3 months ago
2
merge_read_counts() function should have a robust regex expression for matching sample_names to filenames.

#222 RodolfoSalido opened 3 months ago
0
Consider refactoring KLSampleSheet class to use ABC module

#221 charles-cowart opened 3 months ago
0
Improve logging support for metapool

#220 charles-cowart opened 3 months ago
0
Sample sheet support for new SampleContext section

#219 AmandaBirmingham closed 3 months ago
1
Brings up to date with current master

#218 AmandaBirmingham closed 3 months ago
0
Python 3.11 doesn't support nose tests used in this repo.

#217 charles-cowart opened 3 months ago
0
Remove seqpro binaries.

#216 charles-cowart opened 4 months ago
1
Fixed demuxed sample-sheet generation

#215 charles-cowart closed 4 months ago
1
Bugfix

#214 charles-cowart closed 4 months ago
1
Remove ignore_index=True argument when combining pre-prep files.

#213 RodolfoSalido closed 4 months ago
0
Make columns in [Bioinformatics] w/boolean values case-insensitive.

#212 charles-cowart closed 4 months ago
1
Boolean values in [Bioinformatics] section are now case-insensitive.

#211 charles-cowart closed 4 months ago
1
Removed non_host_removal & fraction_non_human from output

#210 charles-cowart closed 4 months ago
2
Remove legacy columns from seqpro output.

#209 charles-cowart closed 4 months ago
1
Validate against duplicate sample-info-file columns

#208 charles-cowart opened 5 months ago
1
Dev metaT notebook

#207 RodolfoSalido closed 3 months ago
2
replicate [Data] columns reimplemented like Katharoseq

#206 charles-cowart opened 6 months ago
0
migrate post-metapool validation into metapool

#205 charles-cowart closed 4 months ago
1
update seqpro

#204 charles-cowart opened 6 months ago
0
[Bioinformatics] section validation

#203 charles-cowart opened 6 months ago
1