Skip to content

Issues: rotary-genomics/rotary

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

27 Open 53 Closed
27 Open 53 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

Rotary Hangs When No Contigs Pass Coverage Filter bug Something isn't working
#199 opened Jul 2, 2024 by LeeBergstrand
1
@LeeBergstrand
1
Readme Demo Data Download Fails bug Something isn't working
#182 opened May 31, 2024 by LeeBergstrand
@jmtsuji
1
Move to less threads per sample for multi-sample runs. enhancement New feature or request
#176 opened May 28, 2024 by LeeBergstrand
@LeeBergstrand
6
Add Checkm2 db version to Checkm2 database long_term
#166 opened May 9, 2024 by LeeBergstrand
Metagenomics Mode (MetaFlye and Binning) long_term
#160 opened Apr 19, 2024 by LeeBergstrand
5
Improve run reports for rotary
#157 opened Apr 19, 2024 by LeeBergstrand
6
Address TODOs in the Snakefiles
#156 opened Apr 19, 2024 by LeeBergstrand
Improve Documentation For aggregate_contigs in circularize.smk documentation Improvements or additions to documentation
#151 opened Apr 9, 2024 by LeeBergstrand
@jmtsuji
Re-consider the symlinking paradigm used in rotary
#139 opened Feb 22, 2024 by jmtsuji
@LeeBergstrand @jmtsuji
Pipeline tries to re-run from QC when re-started bug Something isn't working
#134 opened Feb 19, 2024 by jmtsuji
QC read files deleted too early bug Something isn't working
#132 opened Feb 15, 2024 by jmtsuji
@LeeBergstrand @jmtsuji
24
Simplify Python code within certain snakemake rules enhancement New feature or request
#120 opened Feb 13, 2024 by jmtsuji
6
Move to Snakemake 8.0
#111 opened Jan 4, 2024 by LeeBergstrand
1
1
Should we consider adding a simple setting to completely skip short and/or long read QC?
#101 opened Dec 19, 2023 by LeeBergstrand
Add basic PacBio support? enhancement New feature or request
#96 opened Dec 12, 2023 by jmtsuji
Basic test suite for rotary
#95 opened Dec 12, 2023 by jmtsuji
@LeeBergstrand @jmtsuji
2
Check if decontamination genome references need to be in forward and reverse complement orientation
#93 opened Dec 12, 2023 by jmtsuji
@jmtsuji
Report read QC stats
#91 opened Dec 12, 2023 by jmtsuji
@LeeBergstrand
12
Warn about multi-strain contamination based on CheckM2 stats
#89 opened Dec 12, 2023 by jmtsuji
@jmtsuji
Nanopore Read Decontamination enhancement New feature or request
#84 opened Nov 23, 2023 by LeeBergstrand
@LeeBergstrand @jmtsuji
9
Make a separate config file with database version information
#78 opened Nov 9, 2023 by jmtsuji
Improve logging of required coverage thresholds for contigs
#68 opened Oct 24, 2023 by jmtsuji
@jmtsuji
Allow for mixture of samples with or without short-read data.
#59 opened Oct 20, 2023 by LeeBergstrand
1
Additional Flags to Run_One
#51 opened Oct 18, 2023 by LeeBergstrand
2
Update dependancy versions
#50 opened Oct 18, 2023 by LeeBergstrand
ProTip! Find all open issues with in progress development work with linked:pr.