v2.0.0 - 2026-06-23

What's Changed

• Template update for nf-core/tools v2.14.1 by @WackerO in #273
• Show >10 contrasts in report by @pinin4fjords in #272
• Fix pagination on samples table by @pinin4fjords in #274
• Fix gprofiler2 genesets default object by @WackerO in #278
• Bump shinyngs, fix contrasts passed to app creation by @pinin4fjords in #280
• Dev by @bjlang in #282
• Add exclusions for 3.0.1 template update by @pinin4fjords in #299
• Fix-nf-core.yml structure by @mashehu in #300
• Merging template updates by @pinin4fjords in #303
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #301
• small gprofiler2 bugfix by @WackerO in #289
• Disallow TXT files by @WackerO in #304
• Add limma for rnaseq by @KamilMaliszArdigen in #286
• add additional reference to wiki article for MAD by @davidecarlson in #332
• Remove g:profiler colons in docs by @WackerO in #330
• Fix report volcano plots by @WackerO in #342
• Add pipeline-level nf-tests by @atrigila in #343
• Fix replacement of NA sub-strings in blocking variable by @atrigila in #344
• Add plots by biotype by @atrigila in #346
• Update test full profile by @nschcolnicov in #348
• Add software versions in nf-test and check column presence in .Rmd by @atrigila in #359
• Add a warning in the RMD report when some rows are lost after merging Diff and Fatures tables by @alanmmobbs93 in #354
• Updated all nf-core modules and subworkflows by @nschcolnicov in #374
• Update local modules by @nschcolnicov in #380
• POC contrasts csv -> yaml by @nschcolnicov in #382
• Update tabulartogseachip by @nschcolnicov in #412
• Add immunedeconv module by @nschcolnicov in #421
• Contrasts schema validation by @nschcolnicov in #410
• integrate subworkflows into pipeline by @suzannejin in #430
• Template merge 3.2.0 by @atrigila in #434
• Update nf-core modules with new nftests by @nschcolnicov in #420
• update modules by @nschcolnicov in #437
• Integrate subworkflows into pipeline by @suzannejin in #431
• Validate YML contrasts by @atrigila in #436
• Initialized formula based contrast by @nschcolnicov in #440
• Add variancepartition/dream by @atrigila in #446
• NOMERGE simplify toolsheethandling by @pinin4fjords in #448
• Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in #454
• feat: allow usage of strings for makeContrasts in DREAM by @atrigila in #450
• Add toolsheet-related implementations by @suzannejin in #443
• Nf core template update 3.3.1 by @SusiJo in #468
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in #467
• Enable LIMMA handling formulas by @atrigila in #462
• Add formula to DESEQ2 by @atrigila in #473
• Fix: convert NA values to False in sample metadata table by @antoniasaracco in #489
• POC: feat: add dropdown menu in pca by @atrigila in #500
• Issue 492 by @antoniasaracco in #498
• Fix tabs by @grst in #501
• Update documentation & minor report fixes by @SusiJo in #477
• Add Decoupler by @antoniasaracco in #510
• Create a single table for differentially expressed genes instead of s… by @antoniasaracco in #509
• expose dream options by @atrigila in #517
• Replace RMARKDOWNNOTEBOOK with QUARTONOTEBOOK by @delfiterradas in #522
• Allow zero-intercept models in contrasts schema by @grst in #513
• Improve formula regex to match random effects and functions by @grst in #527
• Issue 345 by @antoniasaracco in #523
• WIP: improve reports by @grst in #495
• Update variancepartition/dream module to allow non-count data by @delfiterradas in #559
• multi-config by @suzannejin in #470
• Update module: propr/propd by @ninaxiong11 in #556
• Important! Template update for nf-core/tools v3.5.1 by @nf-core-bot in #563
• Issue 514 by @antoniasaracco in #562
• Enable complex contrasts in DESeq2 by @delfiterradas in #566
• Update shinyngs modules by @delfiterradas in #569
• Autoformat differential abundance report by @delfiterradas in #576
• Fix VARIANCEPARTITION_DREAM table by @atrigila in #577
• Enable tooltips in volcano plot and fix metadata column filtering by @delfiterradas in #575
• Allow lfc_threshold to be a float by @atrigila in #582
• Allow sample to be an integer, apply module updates by @delfiterradas in #581
• Option to disable filtering by @atrigila in #583
• Fix default parameters for limma/dream by @grst in #603
• Update paramsheet pattern to support .yml extensions by @grst in #600
• Upset plots by @antoniasaracco in #595
• Show gene name on volcano plot hover by @atrigila in #615
• Report filtered QC stats by @atrigila in #614
• Replace dendogram by @antoniasaracco in #586
• Improve caching behaviour for processes usingVALIDATOR outputs by @atrigila in #619
• Render report when using dream by @delfiterradas in #607
• Quarto report: improve scree plot by @atrigila in #620
• Create a single table for differentially expressed genes by @delfiterradas in #580
• Sort genes by p-value by default in quarto report by @delfiterradas in #625
• Split zero intercept dream tests to avoid running out of memory by @delfiterradas in #631
• Rename transcript_length_matrix param to feature_length_matrix by @delfiterradas in #633
• Remove deseq2_cores parameter by @delfiterradas in #628
• Update documentation by @delfiterradas in #626
• Boxplots migration by @atrigila in #613
• Harmonize --contrasts and --contrasts_yml by @atrigila in #652
• docs: update parameters description by @atrigila in #653
• Issue 518 by @antoniasaracco in #649
• Reorganize test structure by @suzannejin in #655
• reverting paramsheet to profiles by @suzannejin in #644
• clean workflow output by @suzannejin in #664
• Remove immunedeconv by @delfiterradas in #659
• Harmonize the feature name columns params by @delfiterradas in #646
• Add description for each method by @atrigila in #675
• Update subworkflows by @suzannejin in #680
• Centralized option to set seed for all non-deterministic methods by @atrigila in #672
• Fix intercept in deseq2 by @atrigila in #684
• Improve study_type docs by @atrigila in #683
• Change round_digits default by @atrigila in #681
• Add option to disable sections in the quarto report by @delfiterradas in #638
• Improve abundance type docs and schema description by @atrigila in #686
• Add profiles for generic matrix by @grst in #692
• Bump dream module by @delfiterradas in #689
• Emit individual channels from inner workflow by @pinin4fjords in #687
• Fix data flow for generic_matrix study type by @grst in #694
• migrate to new workflow outputs by @suzannejin in #662
• Put variable of interest first in zero intercept constrasts for limma and dream by @delfiterradas in #702
• Bump shinyngs modules by @delfiterradas in #704
• Update modules to use seqera containers by @atrigila in #705
• Unify de params by @suzannejin in #676
• Drop misleading 'Error: null' from paramset validation failure by @pinin4fjords in #723
• docs: add DREAM/decoupler citations and small usage fixes by @pinin4fjords in #715
• docs(profiles): explain dream_apply_voom defaults in rnaseq vs generic_matrix by @pinin4fjords in #721
• Fix -stub-run by patching shinyngs/validatefomcomponents stub block (#717) by @pinin4fjords in #722
• Schema completeness fixes for issue #712 by @pinin4fjords in #716
• Important! Template update for nf-core/tools v4.0.2 by @nf-core-bot in #707
• Important! Template update for nf-core/tools v4.0.0 by @nf-core-bot in #706
• fix(schema): model comma-separated report_file in pattern by @pinin4fjords in #726
• Workflow robustness: matrix-copy ternary + unguarded .branch (closes #713) by @pinin4fjords in #720
• refactor(report): consolidate helpers and modernise the default qmd by @pinin4fjords in #729
• feat: enable propd differential method and grea functional method by @pinin4fjords in #727
• docs(metro): regenerate pipeline metro map against current dev (#710) by @pinin4fjords in #730
• docs(metro): use animated SVG with PNG fallback in README by @pinin4fjords in #731
• docs(metro): bump to nf-metro 0.7.2 and re-render by @pinin4fjords in #732
• Update variancepartition/dream module and abundance_differential_filter subworkflow by @delfiterradas in #734
• Version bump 2.0.0 by @atrigila in #736
• Fix conda failing tests by @atrigila in #738
• Fix observation table column width for columns with NA by @grst in #739
• Disable implicit parallelism in dream by @delfiterradas in #743
• Reply reviewer's comment for 2.0.0 by @atrigila in #745
• Release 2.0.0 by @atrigila in #737

New Contributors

• @mashehu made their first contribution in #300
• @KamilMaliszArdigen made their first contribution in #286
• @atrigila made their first contribution in #343
• @nschcolnicov made their first contribution in #348
• @SusiJo made their first contribution in #468
• @grst made their first contribution in #501
• @ninaxiong11 made their first contribution in #556

Full Changelog: 1.5.0...2.0.0