v0.7.0

Change

• A more modular config file structure
• TimeTrees are no longer visualized, only ancestral sequences fro each cluster are identified and exported for nexus file generation.

Fixed

• Repaired how the phylogeny report is presented with quarto, there where some command chunks that were not running (eval: false)

v.0.6.0

Changed:

• Quarto rendered HTML replaces static PDFs of phylogeny annotated with clusterIDs.
• Tidied up the module structure to be grouped by workflows.

v.0.5.0

Changed:

• Quarto rendered HTML replaces static PDFs of phylogeny annotated with clusterIDs.
• Tidied up the module structure to be grouped by workflows.

v.0.4.0 (tbd)

Changed:

v0.3.0

Removed

• Removed the TB-Profiler update module and now the update happens within each process to prevent errors the new versions of TB-profiler was producing.
• Corrected the conda enviornment to downgrade BCFtools to a version that TB-Profiler can use.

v0.2.0

This is a functioning version of the RutiSeq-nf workflow. While it still does not perform everything that is planned, the principle workflow is performed and can be executed successfully.

Fixed:

• Conda environment compiling corrected, although TB-Profiler can create issues with BCFtools (which needs to be downgraded to v1.12). Manual correction is possible when this occurs.
• TB-profiler updated to newest version (v6.6.3) to comply with most recent TBDB and WHO database (WHO-V2-Strict, 2025-04-22)
• Path to matrix for data delivery preparation

Changed:

• Added flags to shell scripts (bin/shell/create-variable-region-nexus.sh; bin/shell/create-variable.region.nexus.w.MRCA.sh)

To Do:

• Update docker and singularity/apptainer containers using seqera container tool

v0.1.0

Added:

• Negative control result summary (reads statistics, taxonomy, tb-profiler, mtbseq)
• Documentation of the version controls and description for each module

v0.0.9

Update nextflow.config

v0.0.8

Changed

• Additional controls to remove genomes (based on defined parameters of coverage depth and breadth), in addition to any genomes that display any mixed lineage as defined by TB-Profiler
• How genomes are partitioned into lineages for pairwise analysis as its own module

Fixed

• Rscript that was generating duplicates of each entry.

v.0.0.7

Continued early development. This release is fully functioning SINGLE_WF() and has been tested on 400-1500 genomes at a single point. On average 400 genomes required 17h for the single_WF().

Updated

• Modified how intermediate files emitted that are not required for the final results re handled to prevent buildup of littering files