v1.0.1 Ter

Fixing some bugs from the release.

What's Changed

• v1.0.0 fixes by @FerriolCalvet in #380

Full Changelog: v1.0.0...v1.0.1

v1.0.0 Ter

This release contains a very complete set of analysis and QCs.
Many of them are updated versions of the earlier ones together with some code cleaning and new features.

What's Changed

• Diverse updates and fixes by @FerriolCalvet in #335
• Add contamination check by @FerriolCalvet in #317
• Add several plotting scripts by @FerriolCalvet in #333
• New mutation density calculation: closes #272 by @koszulordie in #338
• Add SigProfilerMatrixGenerator by @FerriolCalvet in #345
• Set minimum mutations per sample threshold by @FerriolCalvet in #346
• Automatically parse PMEAN and PSTD if available by @FerriolCalvet in #349
• Update feature groups input definition by @FerriolCalvet in #350
• Add several plotting updates by @FerriolCalvet in #354
• Add mutation densities QC plots by @rochamorro1 in #356
• LICENSE, linting and other minor updates by @FerriolCalvet in #347
• Allow the option to plot selection and saturation at the level of groups by @FerriolCalvet in #366
• fix bug that outputted empty maf files by @FerriolCalvet in #367
• Add globalloc synonymous numbers QC by @FerriolCalvet in #370
• fix bug in redefinition of panel with subgenic elements by @FerriolCalvet in #373
• Update container for HDP signature extraction by @FerriolCalvet in #362
• Add Nanoseq masks as filters by @m-huertasp in #374
• add test setup and first tests by @FerriolCalvet in #375
• New release: v1.0.0 Ter by @FerriolCalvet in #377

New Contributors

• @rochamorro1 made their first contribution in #356
• @m-huertasp made their first contribution in #374

Full Changelog: v0.2.0-alpha...v1.0.0

Complete public release

Include more detailed documentation on deepCSA requirements, steps and outputs, improve code readability among many others.

What's Changed

• First release by @FerriolCalvet in #289
• First pre-release merge by @FerriolCalvet in #303
• Documenting and cleaning by @FerriolCalvet in #299
• Ensure POSTPROCESSVEPPANEL in output by @FerriolCalvet in #311
• Update mutation rate to mutation density by @FerriolCalvet in #307
• fix panel annotation bug by @FerriolCalvet in #313
• Add more complete docs by @FerriolCalvet in #306
• Allow gene selection in consensus by @FerriolCalvet in #316
• general structure updates by @FerriolCalvet in #315

Full Changelog: v0.1.0-alpha...v0.2.0-alpha

First release

First release before re-structuring prefix definitions and lib directory.
Version of the pipeline used for the normal bladder urothelium project.

What's Changed

• VCFs annotated by @FerriolCalvet in #8
• update by @rblancomi in #12
• Add lasts preparations for compute depths subworkflow by @FerriolCalvet in #18
• Basic mutation preprocessing finished by @FerriolCalvet in #19
• Basic processing working all subworkflows initialized by @FerriolCalvet in #20
• Major update deepCSA by @FerriolCalvet in #26
• add all sections working to date by @FerriolCalvet in #34
• add depths and panels section by @rblancomi in #33
• Add mutation rate subworkflow by @FerriolCalvet in #41
• 43-remove configuration redundancy by @FerriolCalvet in #44
• dev/omegamulti by @FerriolCalvet in #51
• dev/muts2sbs by @FerriolCalvet in #52
• fix: mutation rate computed with SNVs and indels by @rblancomi in #61
• Add mSigHDP by @FerriolCalvet in #63
• Plot basic summary statistics by @FerriolCalvet in #83
• fix: handle bedtool offset issue by @FedericaBrando in #88
• Add omega global loc by @FerriolCalvet in #90
• Improve config params focussed by @FerriolCalvet in #91
• Add mutated epithelium computation (breaking changes) by @FerriolCalvet in #81
• [FIX] Bedtools merge in CREATECUSTOMBED process by @FedericaBrando in #92
• add: panel composition adjusted mutrate and Kb by @rblancomi in #96
• Use VAF from all molecules by @FerriolCalvet in #102
• add: oncodrive3d preprocessing module by @FerriolCalvet in #101
• Update Oncodrive3D run and add Oncodrive3D plotting module by @St3451 in #106
• ADD proportion of mutated genomes from VAF by @koszulordie in #105
• 104 add indels method by @FerriolCalvet in #109
• BREAKING CHANGES Add pileup step in the pipeline by @FerriolCalvet in #111
• Input BAM for running pileup within the pipeline by @FerriolCalvet in #110
• add fixes by @FerriolCalvet in #124
• add positive selection side plots + nextflow version to 24.04 by @FerriolCalvet in #121
• Add option for custom gene groups in omega by @FerriolCalvet in #127
• Add option to restrict all analysis to custom BED file by @FerriolCalvet in #130
• Update the scripts to handle NAs in mutations by @FerriolCalvet in #131
• Add hotspots to mice by @FerriolCalvet in #134
• Mice working by @FerriolCalvet in #136
• Add working for mice, omega for hotspots and omega plotting by @FerriolCalvet in #138
• Add updates from dev branch before testing by @FerriolCalvet in #140
• add expected epithelium calculation by @AxelRosendahlHuber in #141
• working version in the IRB cluster by @FerriolCalvet in #144
• Reorganize subworkflows input and fix mutrate bug by @FerriolCalvet in #147
• Minor fixes in depths by @FerriolCalvet in #154
• Add fixes for updated omega global loc by @FerriolCalvet in #152
• Add computation of unbiased VAF by @FerriolCalvet in #158
• Add cconfigs for CHIP by @andrianovam in #168
• fix in BED panel creation from TSV by @FerriolCalvet in #170
• Add protein2dna mapping by @FerriolCalvet in #211
• Another fix to omega globalloc by @FerriolCalvet in #209
• Quick fix to make sample names match by @FerriolCalvet in #219
• Add dNdScv and expected mutated genomes to dev by @FerriolCalvet in #217
• Add hotspot annotations by @FerriolCalvet in #218
• Split not_in_panel into two filters by @FerriolCalvet in #222
• Add cohort_n_rich_threshold by @FerriolCalvet in #223
• Add option to compute omega for smaller gene areas (not sites) by @FerriolCalvet in #228
• CODE-REVIEW | NF lint : Implement topics, fix statement outside top-level declaration by @FedericaBrando in #232
• Add comparison per site by @FerriolCalvet in #234
• CODE-REVIEW | 2nd iteration | NF linting, fix nextflow_schema and configs by @FedericaBrando in #238
• fix: update workflow name in configs by @FerriolCalvet in #241
• Compute omega for TERT by @FerriolCalvet in #239
• Add site comparison of expected vs observed by @FerriolCalvet in #245
• Add updated filters to dev by @FerriolCalvet in #249
• Add optional step to blacklist mutations by @FerriolCalvet in #254
• Update mutations plot format by @FerriolCalvet in #255
• Add domain BED automated generation by @FerriolCalvet in #253
• Add new mutated genomes computation by @FerriolCalvet in #251
• 260 specific consequence type filters for tert promoter in proportion of mutated epithelium by @koszulordie in #261
• Fix incorrect plotting of mutational profile by @FerriolCalvet in #263
• Define SNP flag based on gnomAD by @FerriolCalvet in #266
• Create single environment for bin python scripts. by @FedericaBrando in #267
• Write all versions of mutational profiles by @FerriolCalvet in #271
• Separation of artifactual filter from somatic filter by @FerriolCalvet in #280
• Separate depths script into summary and within gene plotting by @FerriolCalvet in #281
• Update naming of concatenated matrices by @FerriolCalvet in #283
• Add HDP signature extraction by @FerriolCalvet in #269
• Add downsampling and regressions by @FerriolCalvet in #258
• Add no_filter option working by @FerriolCalvet in #291

New Contributors

• @rblancomi made their first contribution in #12
• @FedericaBrando made their first contribution in #88
• @St3451 made their first contribution in #106
• @koszulordie made their first contribution in #105
• @AxelRosendahlHuber made their first contribution in #141
• @andrianovam made their first contribution in #168

Full Changelog: https://github.com/bbglab/deepCSA/commits/v0.1.0-alpha