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

37 Open 42 Closed
37 Open 42 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

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
Configure Github Actions yaml file to only submit one test when a pull-request is open for a branch done Issues that have been addressed in dev branch, but not reflected in master branch enhancement New feature or request priority_2
#109 opened Nov 25, 2024 by harmonbhasin
1
Change resources.config labels to be more accurate enhancement New feature or request priority_3
#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_3
#104 opened Nov 20, 2024 by willbradshaw
@harmonbhasin
summarize-multiqc-pair doesn't give information for each read pair separately anymore.
#102 opened Nov 19, 2024 by simonleandergrimm
@simonleandergrimm
1
Use zapier (or some other automation tool) to make a post on twist everytime the master branch has changed. enhancement New feature or request priority_3
#97 opened Nov 15, 2024 by harmonbhasin
Make generate_samplesheet take in single-read data done Issues that have been addressed in dev branch, but not reflected in master branch enhancement New feature or request
#92 opened Nov 13, 2024 by simonleandergrimm
@simonleandergrimm
Update index workflow to pass a subpath to extract the kraken2 DB done Issues that have been addressed in dev branch, but not reflected in master branch enhancement New feature or request priority_3
#91 opened Nov 13, 2024 by harmonbhasin
@harmonbhasin
1
Migrate some of README and create a FAQ in the Wiki portion of repo enhancement New feature or request priority_3
#90 opened Nov 13, 2024 by harmonbhasin
@harmonbhasin
Implement an end-to-end test using nf-test enhancement New feature or request priority_1
#88 opened Nov 13, 2024 by harmonbhasin
@harmonbhasin
Investigate weird behavior between bbmerge and bowtie2 bug Something isn't working priority_1
#87 opened Nov 13, 2024 by harmonbhasin
@harmonbhasin
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
Consider swapping in Falco for FastQC enhancement New feature or request in-progress Mark this label when the assignee is actively working on this item.
#78 opened Oct 21, 2024 by mikemc
@harmonbhasin
1
Thinking through behavior regarding transgenic and other problematic sequences enhancement New feature or request
#77 opened Oct 21, 2024 by mikemc
1
Outputting all pre-deduplicated reads in the HV workflow enhancement New feature or request priority_1
#76 opened Oct 18, 2024 by mikemc
2
Make COUNT_ALIGNMENT_DUPLICATES use more clever parent selection. enhancement New feature or request priority_2
#75 opened Oct 16, 2024 by harmonbhasin
Run FASTQC on a subset of reads enhancement New feature or request in-progress Mark this label when the assignee is actively working on this item. priority_2
#74 opened Oct 16, 2024 by harmonbhasin
@harmonbhasin
3
Find another tool for deduplication (that operates similarly to Clumpify) enhancement New feature or request priority_3
#72 opened Oct 16, 2024 by harmonbhasin
1
Plan for getting mgs-workflow to take in Nanopore data. enhancement New feature or request
#69 opened Oct 14, 2024 by simonleandergrimm
@simonleandergrimm
3
Feature request - module for generating coverage data enhancement New feature or request priority_3
#68 opened Oct 9, 2024 by lennijusten
1
Checking if BBTools' parallel compression is enabled enhancement New feature or request
#66 opened Oct 7, 2024 by mikemc
Our execution timeline is slightly different from nextflow's execution timeline. bug Something isn't working priority_3
#64 opened Oct 7, 2024 by harmonbhasin
Cut down working and output directories enhancement New feature or request priority_1
#52 opened Sep 18, 2024 by willbradshaw
ProTip! Type g i on any issue or pull request to go back to the issue listing page.