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Verify forward/backward compatibility for bioconda/somatem and github/somatem for dev

Status: Open.

Task

#109 In treangenlab/somatem;

· ppreshant opened on Apr 6, 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

Work on nextflow run logistics: default profile (local, micromamba), store CLI output and .nextflow.log

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#104 In treangenlab/somatem;

· ppreshant opened on Apr 2, 2026

lemur database download issue: bioconda/somatem

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#103 In treangenlab/somatem;

· microbemarsh opened on Mar 26, 2026

·  

v2.0: publication ready

Check directory compatibility (gdrive download etc.) for bioconda/somatem

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

parameter valuesSetting proper defaults or changing parameters that go into a particular toolSetting proper defaults or changing parameters that go into a particular tool

Status: Open.

Task

#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 (for better error msg & 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: somatem pipeline on bioconda and for preprint

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.

Feature

#84 In treangenlab/somatem;

· microbemarsh opened on Feb 26, 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