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Use separate modules for flye coassembly and minigraph before rhea

enhancementNew feature or requestNew feature or request

nice-to-havefeature requests/enhancements that are not too significant but would be nice to have.feature requests/enhancements that are not too significant but would be nice to have.

Status: Open.

#122 In treangenlab/somatem;

· ppreshant opened on May 14, 2026

Expose all parameters from individual tools in somatem

Status: Open.

#116 In treangenlab/somatem;

· ppreshant opened on Apr 27, 2026

Distill the 3 species detection tables into a single output file with a python/pola.rs script

Status: Open.

#115 In treangenlab/somatem;

· ppreshant opened on Apr 22, 2026

Add subworkflow for ensemble species detection with 3 taxonomic profilers

Status: Open.

Feature

#107 In treangenlab/somatem;

· ppreshant opened on Apr 6, 2026

Add kente to the pipeline

Status: Open.

#106 In treangenlab/somatem;

· ppreshant opened on Apr 3, 2026

·  

v2.0: publication ready

Combine multiple samples into unified results for comparison : Taxonomic profiling

Status: Open.

Feature

#94 In treangenlab/somatem;

· ppreshant opened on Mar 4, 2026

·  

v2.0: publication ready

assembly mags Bakta encode/decode error

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#90 In treangenlab/somatem;

· microbemarsh opened on Mar 2, 2026

Implement viral, fungal taxonomic profiling with sylph

databasesomething about database: failing downloads, not cacheing properly, taking forever etc.something about database: failing downloads, not cacheing properly, taking forever etc.

enhancementNew feature or requestNew feature or request

Status: Open.

Feature

#74 In treangenlab/somatem;

· ppreshant opened on Jan 9, 2026

·  

v1 release: somatem pipeline on bioconda and for preprint

Revive sylph module, download 3 DBs

databasesomething about database: failing downloads, not cacheing properly, taking forever etc.something about database: failing downloads, not cacheing properly, taking forever etc.

enhancementNew feature or requestNew feature or request

Status: Open.

Feature

#73 In treangenlab/somatem;

· ppreshant opened on Jan 9, 2026

·  

v1 release: somatem pipeline on bioconda and for preprint

Complete documentation in README + Wiki

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

Task

#63 In treangenlab/somatem;

· ppreshant opened on Oct 15, 2025

·  

v1 release: somatem pipeline on bioconda and for preprint

Streamlining/ optimization/ cleanup tasks for future + new features related to nextflow

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#60 In treangenlab/somatem;

· ppreshant opened on Oct 3, 2025

Add latest emu and lemur databases (2025) from Mike

databasesomething about database: failing downloads, not cacheing properly, taking forever etc.something about database: failing downloads, not cacheing properly, taking forever etc.

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#56 In treangenlab/somatem;

· ppreshant opened on Sep 25, 2025