CHANGELOG.md

nf-core/differentialabundance: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.6.0dev - xxxx-xx-xx

Added

• [#358] - Added software version check in nf-tests and gene biotype column check in .Rmd (@atrigila, review by @pinin4fjords)
• [#354] - Warning message within the R Markdown report to control when genes don't have annotation data (@alanmmobbs93). Review by @WackerO and @pinin4fjords.
• [#345] - Plot differentially expressed genes by gene biotype (@atrigila, review by @grst)
• [#343] - Add pipeline-level nf-tests (@atrigila, review by @pinin4fjords and @nschcolnicov)
• [#286] - Integration of limma voom for rnaseq data (@KamilMaliszArdigen, review by @pinin4fjords)

Fixed

• [#358] - Fixed nf-tests not running due to --changed-since HEAD^(@atrigila, review by @pinin4fjords)
• [#344] - Fixed replacement of NA sub-strings (@atrigila, suggested by @BEFH, review by @apeltzer and @nschcolnicov)
• [#342] - Fixed incorrectly colored dots in report volcano plots for logFC thresholds <1 (@WackerO, review by @pinin4fjords)
• [#330] - Fixed broken docs by removing g:profiler colons (@WackerO, review by @pinin4fjords)
• [#304] - Removed TXT file options from nextflow_schema where they are equivalent to TSV to make the input files clearer (@WackerO, review by @pinin4fjords)
• [#299] - Add exclusions for 3.0.1 template update (@pinin4fjords)
• [#289] - Fix missing ch_gene_sets default for gprofiler2 (@WackerO, review by @pinin4fjords)
• [#282] - In order to improve resumability, create a copy of the matrix as an annotation file only if necessary; add original matrix file name to copy name (@bjlang, review by @WackerO)
• [#280] - Bump shinyngs, fix contrasts passed to app creation (@pinin4fjords, review by @WackerO)
• [#274] - Fix pagination on samples table (@pinin4fjords, review by @WackerO)
• [#272] - Show >10 contrasts in report (@pinin4fjords, review by @WackerO)

Changed

• [#374] - Update all modules and subworkflows (@nschcolnicov, review by @pinin4fjords).
• [#348] - Update test_full profile matrix file and indentation of profiles in nextflow.config (@nschcolnicov, review by @WackerO and @pinin4fjords)

v1.5.0 - 2024-05-08

Added

• [#273] - Template update for nf-core/tools v2.14.1 (@WackerO, review by @pinin4fjords)
• [#266] - Fix logging by specifying assays to log (@pinin4fjords, review by @WackerO)
• [#259] - Bump gtf2featureannotation to fix GTF handling error (@pinin4fjords, review by @WackerO)
• [#257] - Added maxquant profile to nextflow.config to make it available (@WackerO, review by @pinin4fjords)
• [#254] - Some parameter changes, added qbic credits (@WackerO, review by @pinin4fjords)
• [#250] - Template update for nf-core/tools v2.13.1 (@WackerO, review by @pinin4fjords)
• [#244] - Add pipeline params for matrixfilter NA options (@WackerO, review by @pinin4fjords)
• [#241] - Template update for nf-core/tools v2.13 (@WackerO, review by @nvnieuwk)
• [#228] - Template update for nf-core/tools v2.12 (@nf-core-bot, review by @pinin4fjords, @WackerO)
• [#222] - Add rounding to all numeric report tables (@WackerO, review by @pinin4fjords)
• [#219] - Template update for nf-core/tools v2.11.1 (@WackerO, review by @pinin4fjords)
• [#197] - Add contributor info to report (@WackerO, review by @pinin4fjords)

Fixed

• [#278] - Fix missing ch_gene_sets when running gprofiler without gene sets (@WackerO, review by @pinin4fjords)
• [#267] - Whitespace fix, remove TODO, also update changelog for release release 1.5.0 (@WackerO, review by @pinin4fjords)
• [#265] - GSEA- pngs and htmls in same place (@pinin4fjords, review by @WackerO)
• [#257] - Fixed FILTER_DIFFTABLE module, updated PROTEUS module to better handle whitespace in prefix param, made docs clearer (@WackerO, review by @pinin4fjords)
• [#254] - Made differential_file_suffix optional (@WackerO, review by @pinin4fjords)
• [#240] - Publish GSEA reports (@pinin4fjords, review by @WackerO)
• [#231] - Update GSEA module to fix butterfly plot bug (@WackerO, review by @pinin4fjords)
• [#226] - Fix DESEQ2_NORM in modules.config (@WackerO, review by @pinin4fjords)
• [#221] - Update shinyngs modules to address density plots issue (@pinin4fjords, review by @maxulysse)
• [#223] - tabulartogseacls fixes (@pinin4fjords, review by @maxulysse)
• [#213] - Fix volcano plot legend (@pinin4fjords, review by @WackerO)
• [#210] - Include Affy timeout fix (@pinin4fjords, review by @WackerO)
• [#208] - Fix resource issues and bump versions (@pinin4fjords, review by @sguizard)

Changed

• [#256] - Release 1.5.0 (@WackerO, review by @maxulysse, @pinin4fjords)
• [#264] - Change FILTER_DIFFTABLE to python because AWK does not correctly filter reliably (@WackerO, review by @pinin4fjords)
• [#232] - Mention missing dots in volcano plot, change rounding, turn off rounding by default (@WackerO, review by @pinin4fjords)

v1.4.0 - 2023-11-27

Added

• [#203] - Transcript lengths for DESeq2 (@pinin4fjords, review by @maxulysse)
• [#199] - Add gprofiler2 module and local differential table filtering module (@WackerO, review by @pinin4fjords)
• [#193] - Add DESeq2 text to report (@WackerO, review by @pinin4fjords)
• [#192] - Add scree plot in report (@WackerO, review by @pinin4fjords)
• [#189] - Add DE models to report (@WackerO, review by @pinin4fjords)
• [#188] - Add option to cluster all features (@WackerO, review by @pinin4fjords)
• [#198] - Document correct RNAseq matrix usage (@pinin4fjords, review by @WackerO)

Fixed

• [#201] - DESeq2/Limma update, fix incorrect column names issue (@WackerO, review by @pinin4fjords)
• [#191] - Fix sample metadata table in the html report not paginating (@davidecarlson, review by @pinin4fjords)
• [#190] - Fix GSEA indent in report (@WackerO, review by @pinin4fjords)

Changed

• [#194] - Change report volcano colors (@WackerO, review by @pinin4fjords)
• [#188] - Update min nextflow version (@WackerO, review by @pinin4fjords)

v1.3.1 - 2023-10-26

Fixed

• [#183] - Fix logging for dendrograms (@pinin4fjords, review by @WackerO)

Changed

• [#182] - Fixed Jon's employer (@pinin4fjords, review by @WackerO)

v1.3.0 - 2023-10-24

Added

• [#124] - Template update for nf-core/tools v2.8 (@pinin4fjords, review by @jasmezz)
• [#129] - Module updates to fit with recent registry changes (@pinin4fjords, review by @maxulysse, @adamrtalbot)
• [#130] - Document reasons for lack of differential expression (@pinin4fjords, review by @jfy133)
• [#131] - Improve gtf to table configurability (@pinin4fjords, review by @WackerO)
• [#136] - Added support for non-Affymetrix arrays via automatic download of SOFT matrices in GEO (@azedinez, review by @pinin4fjords)
• [#137] - Add --sizefactors_from_controls and --gene_id_col for DESeq2 module to modules.config (@WackerO, review by @pinin4fjords)
• [#145] - Template update for nf-core/tools v2.9 (@nf-core-bot, review by @pinin4fjords, @WackerO)
• [#147] - Add Maxquant analysis module (@WackerO, review by @pinin4fjords)
• [#166] - Output a parameter-resolved R Markdown document, as well as rendered HTML (@pinin4fjords, review by @WackerO)
• [#119] - Document sample sheet for Affy arrays (@pinin4fjords, review by @WackerO)
• [#165] - Update subway map (@pinin4fjords, review by @FriederikeHanssen)
• [#135] - workaround OPENBLAS using all cores problem (@pinin4fjords, review by @sateeshperi)
• [#176] - bump shinyngs (@pinin4fjords, review by )

Fixed

• [#116] - Skip outlier detection with low replication (@pinin4fjords, review by @nvnieuwk)
• [#122] - Add spaces to satisfy nf-core download for singularity (@pinin4fjords, review by @WackerO)
• [#127] - [Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv (@ctuni, review by @pinin4fjords)
• [#138]- Fix bugs with --control_features and --sizefactors_from_controls (@WackerO, review by @pinin4fjords)
• [#133] - Sample exclusion options fail due to contrast-wise normalisation (@pinin4fjords, review by @WackerO)
• [#160]- Fix merge conflicts for Template update 2.10 by nf-core-bot (@WackerO, review by @pinin4fjords)
• [#164] - Rlog + other small fixes (@pinin4fjords, review by @drpatelh)
• [#174] - Fix metro map (@pinin4fjords, review by @WackerO)

Changed

• [#179] - Removed shiny app error message for proteus runs (@WackerO, review by @pinin4fjords)
• [#159] - CUSTOM/MATRIXFILTER module update (@WackerO, review by @suzannejin)
• [#154] - RMARKDOWNNOTEBOOK env update (@WackerO, review by @pinin4fjords)
• [#151] - Module update (@WackerO, review by @pinin4fjords)
• [#147] - RMARKDOWNNOTEBOOK env update, SHINYNGS and CUSTOM update (@WackerO, review by @pinin4fjords)

v1.2.0 - 2023-04-19

Added

• [#97] - Allow for subsetting of samples for specific contrasts (@pinin4fjords, reported by @danhalligan-hx, review by @WackerO)
• [#105] - Enabled multiple GMT/GMX files for GSEA (@WackerO, reported by @grst, review by @pinin4fjords)
• [#108] - Add shiny app generation (starting feature set) (@pinin4fjords, review by @WackerO)
• [#110] - Add shiny app outputs to tower.yml (@pinin4fjords, review by @WackerO, @maxulysse)
• [#149] - Update README.md - add ref to nf-core/rnaseq and Affymetrix (@smoe, review by @pinin4fjords)

Fixed

• [#95] - Pipeline doesn't check for gene sets file specification when GSEA is activated (@pinin4fjords, reported by @danhalligan-hx, review by @FriederikeHanssen)
• [#93] - Shouldn't be re-using the single exploratory palette across multiple informative variables (@pinin4fjords, review by @matthdsm)

v1.1.1 - 2023-03-02

Fixed

• [#89] - Sanitise for differential (@pinin4fjords, review by @WackerO)

v1.1.0 - 2023-02-22

Added

• [#63] - Add git CI matrix for different test profiles to run (@WackerO, review by @pinin4fjords)
• [#60] - Add Affymetrix analysis modules, observation_name_col, make GTF optional, closing [#47], [#46], [#66] (@pinin4fjords, review by @apeltzer)
• [#70] - Array integration final bits: density plot improvement, output paths (@pinin4fjords, review by @matthdsm, @WackerO)

Fixed

• [#55] - Don't drop dimensions in report with single informative variable (@pinin4fjords, review by @mashehu)
• [#57] - Update module shinyngs/validatefomcomponents and bump other shinyngs modules to resolve [#56] (@WackerO, review by @pinin4fjords)
• [#65] - Update shinyngs modules to latest to resolve palette issues reported by @Shellfishgene (@pinin4fjords, review by @mashehu)
• [#67] - Error when contrast is blocking by multiple variables (@pinin4fjords, reported by @clstacy, review by @jfy133)
• [#71] - Add palette options, bring full check.names fixes from upstream, closing [#68] reported by @Shellfishgene, [#69] reported by @clstacy. (@pinin4fjords, reported by @clstacy, review by @matthdsm, @WackerO)
• [#73] - Make --matrix, --input, --features accept either CSV,TXT or TSV files as input (@apeltzer, review by @pinin4fjords)
• [#75] - Bump deseq2/differential for check.names fix (@pinin4fjords, review by @apeltzer)
• [#76] - Fix up non-gtf operation using matrix as annotation source (@pinin4fjords, reported by @apeltzer, review by @apeltzer)
• [#82] - Address v1.1.0 pre-release feedback (subway map fixes) (@pinin4fjords, reported by @mashehu)

v1.0.1 - 2023-01-25

• [#49] - Add citation fixes, missing logos, output detail, and trigger Zenodo (@pinin4fjords, review by @apeltzer, @jfy133)

v1.0.0 - 2023-01-23

Initial release of nf-core/differentialabundance, created with the nf-core template.

Added

• [#1] - Set up initial modules, define and validate workflow inputs (@pinin4fjords, review by @WackerO)
• [#4] - Add input checking (@pinin4fjords, review by @WackerO)
• [#5] - Add differential analysis (@pinin4fjords, review by @WackerO)
• [#6] - Add exploratory plotting (@pinin4fjords, review by @WackerO)
• [#7] - Add differential plotting (@pinin4fjords, review by @WackerO)
• [#8] - Establish outputs/ reports (@pinin4fjords, review by @WackerO)
• [#12] - Handle spike sequences correctly (@pinin4fjords, review by @WackerO)
• [#15] - Add filtering module (@pinin4fjords, review by @WackerO)
• [#21] - Gene set analysis (@pinin4fjords, review by @WackerO)
• [#22] - Complete docs- README etc (@pinin4fjords, review by @WackerO)
• [#23] - Complete minimal report content (@pinin4fjords, review by @WackerO)
• [#38] - Complete full-size test data setup (@pinin4fjords, review by @WackerO)
• [#41] - Update citations (@pinin4fjords, review by @WackerO)

Fixed

Dependencies

Deprecated