v2.2.2: 2025.07-2 updated hotfix for the skip-phylo steps

Full Changelog: v2.2.1...v2.2.2

v2.2.1: 2025.07-1 hotfix release

What's Changed

• Adding parameter interpretation table to output.qmd by @Mxrcon in #243
• Hotfix for skip-phylo... param 7eb98b8

Full Changelog: v2.2.0...v2.2.1

v2.2.0: 2025.06 release with usability enhancements and maintenance work

What's Changed

• Update default_params.config by @vrennie in #230
• update the default tree generation mechanism [ci skip] by @abhi18av in #231
• Add a Customizable IQ-TREE option by @Mxrcon in #232
• fix preprocess_multiqc_input.py script by @Mxrcon in #235
• Dev improve docs by @Mxrcon in #239
• Relocate modules and subworkflows (v2.2.0) by @abhi18av in #241

Full Changelog: v2.1.0...v2.2.0

v2.1.0: With optional configs and processes on FASTQ files

What's Changed

• adding sandbox_vm config for user testing by @vrennie in #223
• add a license header for all source files by @abhi18av in #224
• Update bwa_k66.config by @abhi18av in #226
• Add branches for tbprofiler (fastq) and spotyping witin quality_control subworkflow by @abhi18av in #228

Full Changelog: v2.0.0...v2.1.0

v2.0.0: Optimized MAGMA pipeline with NTM support

What's Changed

• Add MTB_L10 reference in the bundled GVCF by @abhi18av in #200
• Iteration for v2.0.0-beta release - update GVCF by @abhi18av in #201
• Remove the custom built who-magma database for tb-profiler by @abhi18av in #203
• Improve strand bias filter for minor/infrequent variants by @abhi18av in #202
• Simplify the samplesheet by @abhi18av in #204
• Compute FASTQ stats from the input samplesheet by @abhi18av in #205
• Enable the ITOL annotations in the tb-profiler command by @abhi18av in #197
• Add clarification for bqsr recaliberated files by @abhi18av in #213
• Structural variants v2 - accommodate transposable elements by @abhi18av in #209
• Update convert_ismapper_to_vcf.py by @vrennie in #214
• Iteration for 2.0.0-beta release by @abhi18av in #206

Full Changelog: v2.0.0-alpha...v2.0.0-beta

v2.0.0-alpha

What's Changed

• Docs update by @abhi18av in #178
• Add a config file for the low memory users by @vrennie in #184
• Release v2.0.0 with updated TBprofiler and new NTMprofiler results by @abhi18av in #191

Full Changelog: v1.1.1...v2.0.0-alpha

Finalise the structural variants computation

What's Changed

• Changes for v1.1.1 by @abhi18av in #170
• Final pre-release documentation tweaks by @abhi18av in #176

Full Changelog: v1.0.2...v1.1.1

Update filtering logic before cohort analysis

What's Changed

• Update the main README by @abhi18av in #160
• Refactor the stats computation and filtering logic by @abhi18av in #161
• Structural variant analysis by @abhi18av in #154

Full Changelog: v1.0.1...v1.0.2

Release with patches for summary scripts

Update reformat_lofreq.py

Fixed an issue where empty VCf files would have the FORMAT tag

v1.0.0: The first major release!

Word of thanks and congratulations!

This major release of the pipeline is possible due to the contributions of @TimHHH @LennertVerboven @abhi18av @vrennie within the TORCH-consortium and the authors would be very glad to receive feedback to improve the overall contributions.

What's Changed

• Rename pipeline to magma and update documentation by @abhi18av in #141

Full Changelog: v0.9.10...v1.0.0