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40 Open 58 Closed
40 Open 58 Closed
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Issues list

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
Run end-to-end test of index, run, and run validation workflow in parallel on Github Actions enhancement New feature or request priority_2
#111 opened Nov 25, 2024 by harmonbhasin
Github Actions node warning enhancement New feature or request priority_3
#110 opened Nov 25, 2024 by harmonbhasin
Change resources.config labels to be more accurate enhancement New feature or request priority_2
#108 opened Nov 25, 2024 by harmonbhasin
Once new testing regime is on dev, update testing setup in single-read branches enhancement New feature or request
#107 opened Nov 23, 2024 by simonleandergrimm
@simonleandergrimm
Move generate_samplesheet to Python done Issues that have been addressed in dev branch, but not reflected in master branch enhancement New feature or request priority_2
#104 opened Nov 20, 2024 by willbradshaw
@harmonbhasin
4
Update index workflow to pass a subpath to extract the kraken2 DB enhancement New feature or request priority_2
#91 opened Nov 13, 2024 by harmonbhasin
@harmonbhasin
2
Migrate some of README and create a FAQ in the Wiki portion of repo enhancement New feature or request priority_2
#90 opened Nov 13, 2024 by harmonbhasin
@harmonbhasin
1
Investigate and improve the pipeline's read-merging behavior bug Something isn't working priority_2
#87 opened Nov 13, 2024 by harmonbhasin
@harmonbhasin
1
Improve logic for subsetting samples in the same group in taxonomic profiling workflow bug Something isn't working priority_3
#81 opened Oct 29, 2024 by harmonbhasin
1
Consider swapping in Falco for FastQC enhancement New feature or request priority_2 time&cost Changes to improve the pipeline's runtime and computational cost
#78 opened Oct 21, 2024 by mikemc
@harmonbhasin
2
ProTip! Find all open issues with in progress development work with linked:pr.