Change Log

Major changes will be documented in this file.

Version 1.5.2 (Sept 3, 2026)

Added

• Add gather module assembly_redox_metal_indexes from KOfam-scan results

• Add gather module mags_redox_metal_indexes from KOfam-scan results

Changed

Fixed

Version 1.5.1 (Sept 2, 2026)

Added

• Add module assembly_redox_metal_indexes for index computation at assembly level using KOfam-scan

• Add module mags_redox_metal_indexes for index computation at binning level using KOfam-scan

Changed

Fixed

Version 1.4.3 (May 28, 2026)

Added

Changed

Fixed

• minor fix on gathering kaiju and redox metabolic indexes

Version 1.4.3 (May 29, 2026)

Added

Changed

Fixed

• Fixed mags_hmmsearch gather output to standard presence/absence gene matrix

• Fixed gathering logic in kaiju,funprofiler,redox_metal_indexes_rb,mifaser

Version 1.4.2 (May 28, 2026)

Added

Changed

• Changed variable type in metal_indexes_rb for R downstream analysis

Fixed

Version 1.4.1 (May 19, 2026)

Added

• Add gather option to kofam_scan package at the bin-based stream

Changed

Fixed

Version 1.3.6 (Mar 26, 2026)

Added

Changed

• Renamed gather func & inner function for consistency

• Renaming smk output files & 2nd rule in redox_metal_plasticity_index module

Fixed

Version 1.3.5 (Mar 25, 2026)

Added

Changed

• Renamed module metal_indexes_rb to redox_metal_indexes and tool from rmi_rpi_indexes to redox_metal_plasticity_index

• Renaming rules, functions according to new namings, and variables

Fixed

Version 1.3.4 (Mar 24, 2026)

Added

Changed

Fixed

• Minor fix to nans in NO_metal exception

• Minor fix to incosistent args namings

Version 1.3.3 (Mar 19, 2026)

Added

Changed

Fixed

• Fix rpi to account for unique Metal pairs

Version 1.3.2 (Mar 13, 2026)

Added

• Added possibility to subfolder in get_sample_results

Changed

• Renamed gather function metal_index_rb to rmi_rpi_indexes & change in gm_gather

• Removed cat raw_reads lanes in gm_setup & Change in --move_and_rename args flag

Fixed

• Fix typo on gather_mags_recognizer

• Fix issue related to gather_rmi_rpi_indexes

Version 1.3.1 (Mar 06, 2026)

Added

Changed

• Removed DRAM from mags_functional_annotation module

Fixed

• Env parameter for snakefile (BBmap & Bowtie2 shrinked)

Version 1.3.0 (Feb 18, 2026)

Added

• Add new module for redox-metabolix & palsticity index computation

Changed

Fixed

• Minor fix on single_sample GNU_parallel sh script

Version 1.2.5 (Dec 9, 2025)

Added

Changed

• Changed -l option in kaiju2table command for complete taxonomic information

Fixed

Version 1.2.4 (Dec 1, 2025)

Added

• Add thread limit to funprofiler snakefile, to hamper sourmash threads parlalelization

Changed

• Removed --unit flag from gather command to rely on samples retrieved directly from gmsetup.yaml

• Minor refactors in gathering scripts to accomodate flag change

Fixed

Version 1.2.3 (Nov 25, 2025)

Added

• Added new optional flag --conda_frontend to the prerun command, allowing users to specify which Conda frontend Snakemake should use (conda or mamba).

Changed

Fixed

Version 1.2.2 (Nov 19, 2025)

Added

Changed

Fixed

• Fixed license specification in toml file and geomosaic --version command

Version 1.2.1 (Nov 19, 2025)

Added

• Added new required flag --source to the prerun command to indicate which previous Geomosaic command was executed: unit or workflow. This allows Geomosaic to select the correct configuration file for execution.

Changed

• Removed the optional --unit flag from the prerun command.

Fixed

Version 1.1.4 (Nov 18, 2025)

Added

• Added fmh-funprofiler for functional annotation with pre-defined KO database (Module: func_classification_rb)

Changed

Fixed

Version 1.1.3 (Jan 8, 2025)

Added

Changed

Fixed

• Fixed ARGs-OAP with custom db (Module: func_classification_rb)

Version 1.1.1 (Dec 27, 2024)

Added

• Added ARGs-OAP Tool (Module: func_classification_rb) for read based quantification with custom database as alternative to mi-faser. For detailed documentation please refer to: https://github.com/xinehc/args_oap

Changed

Fixed

Version 1.1.0 (Sep 25, 2024)

First Major Release