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25 Open 61 Closed
25 Open 61 Closed
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Issues list

Package final genomes into a Zip file
#225 opened Oct 3, 2024 by LeeBergstrand
Add more assembly stats?
#224 opened Oct 3, 2024 by jmtsuji
Combine R1 and R2 short read reports?
#222 opened Oct 2, 2024 by jmtsuji
Move thread and RAM configuration out of Config and into Snakemake profiles. enhancement New feature or request
#221 opened Sep 27, 2024 by LeeBergstrand
@LeeBergstrand
3
Move to less threads per sample for multi-sample runs. enhancement New feature or request
#176 opened May 28, 2024 by LeeBergstrand
@LeeBergstrand
7
Add Checkm2 db version to Checkm2 database long_term
#166 opened May 9, 2024 by LeeBergstrand
Metagenomics Mode (MetaFlye and Binning) enhancement New feature or request question Further information is requested
#160 opened Apr 19, 2024 by LeeBergstrand
10
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
25
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
2
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
Warn about multi-strain contamination based on CheckM2 stats
#89 opened Dec 12, 2023 by jmtsuji
@jmtsuji
1
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
Add Conda install and register package with anaconda.
#42 opened Oct 16, 2023 by LeeBergstrand
@jmtsuji
4
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