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Migrate pipeline to nf-core-like dsl2

Status: Open.

#37 In seandavi/curatedMetagenomicsNextflow;

· seandavi opened on Nov 6, 2025

Pin down versions of biobakery that are compatible with each other in docker

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Open.

#36 In seandavi/curatedMetagenomicsNextflow;

· seandavi opened on Oct 30, 2025

Add BAQLaVa to pipeline

enhancementNew feature or requestNew feature or request

Status: Open.

#35 In seandavi/curatedMetagenomicsNextflow;

· seandavi opened on Oct 30, 2025

versioning

Status: Open.

#33 In seandavi/curatedMetagenomicsNextflow;

· lwaldron opened on Sep 11, 2025

MetaPhlAn 4.2.2 with Jan25 db and generation of the rarefied taxonomic profile

Status: Open.

#30 In seandavi/curatedMetagenomicsNextflow;

· fasnicar opened on Jun 20, 2025

HUMAnN regroup table

Status: Open.

#29 In seandavi/curatedMetagenomicsNextflow;

· fasnicar opened on Jun 18, 2025

Include metagenomic assembly and binning

enhancementNew feature or requestNew feature or request

Status: Open.

#22 In seandavi/curatedMetagenomicsNextflow;

· fasnicar opened on Mar 11, 2025

Add GTDB mapping to CMD4

Status: Open.

#18 In seandavi/curatedMetagenomicsNextflow;

· seandavi opened on Mar 6, 2024