Skip to content

Issues: naobservatory/mgs-workflow

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

35 Open 57 Closed
35 Open 57 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

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
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 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
Eliminate BBMap from pipeline 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
Eliminate Trimmomatic from pipeline 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
#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 priority_1 time&cost Changes to improve the pipeline's runtime and computational cost
#122 opened Dec 10, 2024 by 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 enhancement New feature or request priority_2
#104 opened Nov 20, 2024 by willbradshaw
@harmonbhasin
3
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
Thinking through behavior regarding transgenic and other problematic sequences discussion Questions and comments that don't tie directly to a feature request or bug priority_3
#77 opened Oct 21, 2024 by mikemc
3
Outputting all pre-deduplicated reads in the HV workflow enhancement New feature or request priority_2
#76 opened Oct 18, 2024 by mikemc
3
Make COUNT_ALIGNMENT_DUPLICATES use more clever parent selection. enhancement New feature or request priority_3
#75 opened Oct 16, 2024 by harmonbhasin
1
Run FASTQC on a subset of reads enhancement New feature or request priority_1 time&cost Changes to improve the pipeline's runtime and computational cost
#74 opened Oct 16, 2024 by harmonbhasin
@harmonbhasin
4
Find another tool for deduplication (that operates similarly to Clumpify) enhancement New feature or request priority_3
#72 opened Oct 16, 2024 by harmonbhasin
2
ProTip! Follow long discussions with comments:>50.