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Issues list

Optimize cutadapt error-rate parameter and set of adapters trimmed enhancement New feature or request priority_2
#208 opened Feb 28, 2025 by katherine-stansifer
1
Add illustration of alignment-based duplicate annotation documentation Improvements or additions to documentation priority_3
#202 opened Feb 18, 2025 by willbradshaw
Make index reproducible enhancement New feature or request priority_2
#193 opened Feb 11, 2025 by willbradshaw
Check compatible taxids across index tools enhancement New feature or request priority_2
#192 opened Feb 11, 2025 by willbradshaw
Unclear errors when run with incorrect endedness bug Something isn't working priority_2
#190 opened Feb 10, 2025 by jeffkaufman
@willbradshaw
1
Clarifying docs on viral identification subworkflow documentation Improvements or additions to documentation enhancement New feature or request priority_3
#188 opened Feb 7, 2025 by lennijusten
1
Flowcharts not rendering on Github mobile bug Something isn't working documentation Improvements or additions to documentation priority_3
#187 opened Feb 7, 2025 by lennijusten
2
Create test to check if index outputs are compatible with run workflow. enhancement New feature or request priority_1
#176 opened Jan 31, 2025 by harmonbhasin
@harmonbhasin
Use output of COUNT_READS to determine read fraction for subsetting enhancement New feature or request priority_3
#171 opened Jan 30, 2025 by willbradshaw
Restore lost functionality post-streaming enhancement New feature or request priority_1
#170 opened Jan 30, 2025 by willbradshaw
Binaries checked into repo
#164 opened Jan 28, 2025 by jeffkaufman
Handle empty FASTQs more gracefully enhancement New feature or request priority_2
#161 opened Jan 25, 2025 by simonleandergrimm
@simonleandergrimm
Viral host taxon filtering is confusing/counterintuitive
#159 opened Jan 24, 2025 by willbradshaw
Consistency between NCBI taxonomy versions in the kraken and the custom bowtie databases documentation Improvements or additions to documentation
#153 opened Jan 22, 2025 by mikemc
3
Instructions for pruning docker images documentation Improvements or additions to documentation done Issues that have been addressed in dev branch, but not reflected in master branch
#151 opened Jan 22, 2025 by mikemc
@harmonbhasin
1
Create Rust script that calculates read length. Maybe do subsetting for Illumina and also apply it to that. enhancement New feature or request
#143 opened Jan 13, 2025 by simonleandergrimm
@simonleandergrimm
Generate samplesheet missing usage for --group_across_illumina_lanes enhancement New feature or request priority_3
#137 opened Jan 6, 2025 by harmonbhasin
@harmonbhasin
Investigate alternative implementations for SUBSET_READS_PAIRED_TARGET enhancement New feature or request priority_2 time&cost Changes to improve the pipeline's runtime and computational cost
#131 opened Dec 17, 2024 by willbradshaw
Reduce Batch loading times for large reference DBs enhancement New feature or request priority_2 time&cost Changes to improve the pipeline's runtime and computational cost
#130 opened Dec 17, 2024 by willbradshaw
Implement effective masking for BBDuk-based viral screening and move FASTP downstream done Issues that have been addressed in dev branch, but not reflected in master branch enhancement New feature or request priority_1 time&cost Changes to improve the pipeline's runtime and computational cost
#129 opened Dec 17, 2024 by willbradshaw
@harmonbhasin
Eliminate BBMap from pipeline done Issues that have been addressed in dev branch, but not reflected in master branch enhancement New feature or request priority_2 time&cost Changes to improve the pipeline's runtime and computational cost
#128 opened Dec 17, 2024 by willbradshaw
@harmonbhasin
Eliminate Trimmomatic from pipeline done Issues that have been addressed in dev branch, but not reflected in master branch enhancement New feature or request priority_1 time&cost Changes to improve the pipeline's runtime and computational cost
#127 opened Dec 17, 2024 by willbradshaw
@harmonbhasin
Add low-complexity filtering for ONT data.
#123 opened Dec 10, 2024 by simonleandergrimm
Implement data streaming to reduce memory needs enhancement New feature or request in-progress Mark this label when the assignee is actively working on this item. priority_1 time&cost Changes to improve the pipeline's runtime and computational cost
#122 opened Dec 10, 2024 by willbradshaw
@willbradshaw
Create a parent config file enhancement New feature or request priority_2
#119 opened Dec 3, 2024 by harmonbhasin
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