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

v0.9.11-magma: Countdown for v1.0.0

What's Changed

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

Full Changelog: v0.9.10...v0.9.11-magma

v0.9.10: tbprofiler replaces quanttb

What's Changed

• Accommodate optional exit_rif files via use of cloud-execution friendly [ ] pattern by @abhi18av in #136
• Accommodate various blob storages in filtering processes by @abhi18av in #139
• Tweak the main.nf flow and published a merged cohort report by @abhi18av in #140
• Remove quanttb and refactor tbprofiler cohort analysis by @abhi18av in #137

Full Changelog: v0.9.8.2...v0.9.10

v0.9.8.2: Add samplesheet validation

What's Changed

• Add samplesheet validation by @abhi18av in #135

Full Changelog: v0.9.8.1...v0.9.8.2

v0.9.8.1 : Add fastq validation and other improvements

What's Changed

• Add fastq validation (and other improvements) by @abhi18av in #134

Full Changelog: v0.9.8...v0.9.8.1