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Check directory compatibility (gdrive download etc.) for the conda downloaded somatem pipeline

Status: Open.

Task

#98 In treangenlab/somatem;

· ppreshant opened on Mar 17, 2026

Combine individual sample outputs into unified results : Taxonomic profiling

Status: Open.

Feature

#94 In treangenlab/somatem;

· ppreshant opened on Mar 4, 2026

·  

v2.0: publication ready

Chopper: intelligent defaults in the context of 16S

enhancementNew feature or requestNew feature or request

Status: Open.

#93 In treangenlab/somatem;

· ppreshant opened on Mar 3, 2026

·  

v2.0: publication ready

Need a nextflow/nf-core style mechanism to check for absence of files (_better errors ; before tools are run_)

enhancementNew feature or requestNew feature or request

Status: Open.

Feature

#92 In treangenlab/somatem;

· ppreshant opened on Mar 3, 2026

·  

v1 release: Final demo of Somatem

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

Make metagenomescope module: run after rhea

Status: Open.

#84 In treangenlab/somatem;

· microbemarsh opened on Feb 26, 2026

Deployment of Somatem onto google cloud / other cloud services

Status: Open.

#79 In treangenlab/somatem;

· ppreshant opened on Feb 12, 2026

Implement viral, fungal taxonomic profiling with sylph

Status: Open.

#74 In treangenlab/somatem;

· ppreshant opened on Jan 9, 2026

·  

v1 release: Final demo of Somatem

Revive sylph module, download 3 DBs

Status: Open.

#73 In treangenlab/somatem;

· ppreshant opened on Jan 9, 2026

·  

v1 release: Final demo of Somatem

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: Final demo of Somatem

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

Adding dereplicator after creating mags?

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.

Feature

#57 In treangenlab/somatem;

· ppreshant opened on Sep 29, 2025