Feature/Pull Request

Feature/Pull Request We welcome feedback and issue reporting for all bioBakery tools through our Discourse site. For users that would like to directly contribute to the tools we are happy to field PRs to address bug fixes. Please note the turn around time on our end might be a bit long to field these but that does not mean we don’t value the contribution! We currently don’t accept PRs to add new functionality to tools but we would be happy to receive your feedback on Discourse.

Topic	Replies	Views	Activity
Implement download resumption in `humann_databases` Feature/Pull Request	3	260	November 21, 2023
Reduce storage requirements when running HUMAnN Feature/Pull Request	1	327	May 26, 2022
Use nvBowtie instead of bowtie2 Feature/Pull Request	0	414	May 27, 2022
Update HUMAnN for MetaPhlAn 4.2 compatability Feature/Pull Request	3	180	June 16, 2025
Add metaphlan database location to humann3 log file Feature/Pull Request	0	336	July 19, 2022
Performance of HUMAnN Custom Database Creation Feature/Pull Request	2	103	June 20, 2024
Missing `mpa_vOct22_CHOCOPhlAnSGB_202403.tsv` in HUMAnN 4 utility_mapping database Feature/Pull Request	0	26	November 30, 2025
Support for SummarizedExperiment assays Feature/Pull Request	3	52	January 31, 2025
Check for downloaded db Feature/Pull Request	0	97	March 20, 2024
FIX: metaphlan4 bowtie2-build --threads flag bug #229 Feature/Pull Request	0	62	August 22, 2024
Multithreading blasting of unaligned reads Feature/Pull Request	1	37	August 13, 2024
Chocophlan version Feature/Pull Request	0	30	May 8, 2025
A question about the Intermediate results and abundance in MetaPhlAn Feature/Pull Request	0	29	March 3, 2025
KneadData setup.py update to URL reference for TRF.exe Feature/Pull Request	0	26	November 11, 2024
Feature request: phylophlan_write_config_file, force generation of config, despite the lack of a program at PATH Feature/Pull Request	0	20	July 4, 2025
Feature request: allow to put fraction with some parameters Feature/Pull Request	0	11	July 4, 2025
Fixing broken links in readme.md from HUMAnN GitHub repository Feature/Pull Request	0	5	December 9, 2025