deepumicaller - v0.5.0

This release contains few updates mainly related to adding more outputs to get a better summary of the cohort in terms of potential errors, potential off targets and also update specific tools

What's Changed

• v0.5.0 by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/128

Full Changelog: https://github.com/bbglab/deepUMIcaller/compare/v0.4.0...v0.5.0

- Nextflow
Published by FerriolCalvet 6 months ago

deepumicaller - v0.4.0

• Enhanced documentation
• Use nf-schema validation
• new features

What's Changed

• Pull BED files and provide to module by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/95
• Compute the coverage of the discarded BAM by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/101
• Update position of AM filtering by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/97
• separate plotting for purine and pyrimidine in duplex calls by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/106
• Release v0.4.0 by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/115

Full Changelog: https://github.com/bbglab/deepUMIcaller/compare/v0.3.0...v0.4.0

- Nextflow
Published by FerriolCalvet 7 months ago

deepumicaller - v0.3.0

What's Changed

• Fix/recompute depth optimization and vardict by @migrau in https://github.com/bbglab/deepUMIcaller/pull/87
• Add custom read size param by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/88
• code refactoring for n_rich filter by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/93
• Add AM filter, VarDict params and cleaning by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/90

Full Changelog: https://github.com/bbglab/deepUMIcaller/compare/v0.2.0...v0.3.0

- Nextflow
Published by FerriolCalvet 11 months ago

deepumicaller - v0.2.0

What's Changed

• Merge updates in N filtering step and README by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/55
• feat: allow using VEP111 version by @migrau in https://github.com/bbglab/deepUMIcaller/pull/59
• Update family metrics and depth reporting by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/56
• dev/asminusxs to vaf from uniq_mol by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/63
• AS-XS improved + add VAF from unique molecules BAM by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/64
• Additional step + more config options + new filtering of mutations by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/67
• add updates from master to 24.04 branch by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/71
• add 24.04 updates to fix branch by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/72
• Fix samtools sort cache being outputted and add v24.04 updates by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/73
• add quick disambiguation fix with last step by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/77
• Fix bug in calling BED file by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/79
• fix turn of off QCs by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/82
• Remove fastq files from repo by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/86

Full Changelog: https://github.com/bbglab/deepUMIcaller/compare/v0.1.0-beta...v0.2.0

- Nextflow
Published by migrau about 1 year ago

deepumicaller - v0.1.0-beta

First working version of deepUMIcaller. Still some things are missing and it is not fully portable but we are in the process.

What's Changed

• Steps addition by @migrau in https://github.com/bbglab/deepUMIcaller/pull/22
• Merge dev/mutationfilters branch by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/23
• Merge dev/mutsperpos by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/24
• Update low mappability filters by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/39
• Add fix_ns branch by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/47
• Merge first release fixes by @FerriolCalvet in https://github.com/bbglab/deepUMIcaller/pull/48

New Contributors

• @migrau made their first contribution in https://github.com/bbglab/deepUMIcaller/pull/11
• @FerriolCalvet made their first contribution in https://github.com/bbglab/deepUMIcaller/pull/23

Full Changelog: https://github.com/bbglab/deepUMIcaller/commits/v0.1.0-beta

- Nextflow
Published by FerriolCalvet about 2 years ago