The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- #245 Added background gene list to pathway analysis output
- #249 Release 2.4
- #248 Version bumps for release 2.4
- #247 Changed the report text that shows when the gprofiler GMT file could not be downloaded
- #247 Removed hard-coded comment about usage of gprofiler databases KEGG and REAC in the report
- #237 Added Euclidian distance/z-score info to report text/heatmaps; added tables next to heatmaps in case the heatmap plotting does not work
- #229 Added param for clustering (or not) the heatmaps
- #226 Added logic to read newer multiqc files from rnaseq 3.12
- #225 Added param for pathway analysis datasources
- #221 Added padj to volcano hovertext
- #244 Release 2.3 to master, part II (found a bug before actual release)
- #237 Changed geom_jitter to geom_point for volcano plot so that points are accurate
- #233 Release 2.3 to master, part I
- #225 Shortened names of some output files
- #243 Fix missing QBiC logo and css styling in report by adding logo/css params
- #242 Fix path issue in report by adding report_file/references_file params
- #241 Undo fix branch protection bug in order to get precommit test to run
- #240 Fix branch protection bug --> third attempt
- #239 Fix branch protection bug --> second attempt
- #238 Fix branch protection bug
- #237 Fix version in usage docs and remove duplicate datasources in test_custom_gmt.config
- #236 Fixed new multiqc check (in case both the files of the old and new mqc version are present)
- #234 Fixed unnecessary file permission changes from #225
- #228 Fixed text in report
- #229 Fixed cutoff enrichment plot labels, fixed wrong plotMA function being called (also fixed this changelog)
- #225 Fixed too many devices error from tryCatch around normalized heatmaps
- #221 Fixed non-conformable arrays bug, fix wrong volcano colors when no DE genes
- #215 Added gene_name to boxplot titles and filenames; increased threshold before overlapping PCA labels are hidden
- #213 Added smrnaseq input support
- #212 Added computational methods if no --software_versions
- #206 Added logic to decide between rlog and vst, added tryCatch for heatmap saving because this only works unreliably
- #202 Added background list to pathway analysis
- #197 Added gprofiler version string to report
- #196 Added optional
--quoteparameter
- #219 Release 2.2 to master
- #220 Commit suggestions from PR review for release 2.2
- #218 Preparing release 2.2 with version bumps
- #217 For rsem/salmon-imports, when a GTF is sometimes missing gene_names, these are now replaced by gene_ids instead
- #215 Boxplots of genes are now generated from rlog/vst counts instead of raw counts. Also, if batch effect correction is enabled, boxplots will be generated before and after correction
- #214 Added smrnaseq input support -->follow-up to check that the CI test works. Modified smrnaseq testdata to be like QBiC datasets. Updated container env and fixed a resulting bug with include_graphics. Heatmaps are now equally ordered in zip and report
- #211 Replaced heatmaply with pheatmap for static plots and removed kaleido and reticulate from container
- #209 Template update to 2.9, Chromium Falcon; exchanged file.exists for nf-core validation checks; changed round_DE param to int
- #206 Changed < and > to <= and => for logF/pval comparisons, renamed gene_counts_tables/deseq2_library_scaled_gene_counts.tsv to deseq2_library_scaled_gene_counts.tsv and added entry to the folder explanation; renamed param pval_threshold to adj_pval_threshold
- #205 Template update
- #204 Changed relevel path in test_relevel.config to the qbic-pipelines repo
- #203 Switched from Dockerhub to GHCR
- #200 Made software_versions optional
- #198 Changed heatmaps to scale in size automatically
- #212 Fixed movability of interactive gostplots
- #208 Fixed relevel bug, the function should now finally work!
- #207 Fixed check of samples in counts vs metadata
- #206 Added correct plot titles to meanSdPlot (depending on normalization)
- #195 Fixed section error in report
- #192 Added software_version yml functionality
- #191 Added test software_versions.yml files for rsem and salmon
- #188 Added titles to static heatmaps, added labels to static PCA plots
- #176 Added output description to report
- #175 Added nf-core citation to report
- #173 Added GMT file to testdata dir to test #172
- #172 Added option to provide custom gost GMT, for online gost, GMT is downloaded
- #151 Added session info to report
- #149 Added gene names to PA tables
- #148 Added KEGG/REAC versions to report
- #147 Added check for contrast list/metadata comparison
- #145 Added pval threshold param
- #136 Added pytest checks and md5sums to make sure that output stays consistent
- #180 Bump version to 2.1 in some more files
- #179 Release 2.1
- #178 Bump version to 2.1
- #177 Updated usage documentation
- #174 Template update, changed param --metadata to --input
- #169 Changed skip_pathway_analysis to run_pathway_analysis, default false
- #165 -fw entries in multiqc stats are now merged
- #164 Boxplots are now only generated for contrasts in list/matrix file if provided
- #163 Template update, re-added limma, annotationdbi, colorbrewr to env (were previously incorrectly deleted), switched container to mamba
- #159 Changed error messages for non-existing rsem/salmon files
- #151 PCA plots and heatmap are now interactive, volcano and enrichment plots are cleaned up in their layout
- #145 Renamed versions to software_versions
- #188 Fixed cut-off enrichment legends and cut-off volcano ylabs
- #181 Fixed nf-core version test in ci.yml, updated schema.yml
- #167 Corrected 5sum for batcheffect after container update
- #152 Fixed empty qlist for gost query
- #150 Removed human and mouse db from env.yml, both are now installed during pipeline execution if needed
- #134 Corrected some versions
- #132 Bump version to 2.0.1
- #131 Added design_batcheffect.txt
- #130 Added test_batcheffect to github tests
- #131 Changed Sample_preparations.tsv by adding batch column
- #130 Fixed batch effect bug
- #128 Bump versions to 2.0
- #125 Added test_relevel to github tests, added explanation to usage.md that --species is not necessary if skipping pathway analysis
- #123 Export report volcano plots as SVG; save all plots additionally as PDF
- #122 Add searchable/sortable tables to report
- #118 Add parameter "--input_type" (and change --rawcounts to --gene_counts) to process featurecounts, rsem and salmon output from the new rnaseq; add igenomes.config to process different species
- #104 Add parameter "--skip_pathway_analysis"
- Bump versions to 1.4.0dev
- Add parameter "--min_DE_genes"
- #97 Update pipeline to DSL2
- #107 Add parameter "--skip_rlog"
- #111 Added enhanced volcano plots
- #93 Add parameter "--nsubgenes"
- #115 Template update
- #117 Turned LabID optional for report output in RNAseq_report.Rmd
- Removed assets/report_options.yml
- #110 Changed report to use rlog normalization by default, vst is used if --skip_rlog is enabled
- #127 Allgenes files are not introduced in the PA report section anymore except for volcano plots
- #126 Allgenes files are not published in results anymore. Intermediate results are not zipped and published anymore
- #125 Fixed relevel bug
- #124 Combined the different scripts into the report. Manually added the changes from #126 and 127 to the 1script branch as at least the code part is combined from multiple previous scrips into a single one
- #118 Removed blacklist parameter and config and instead added trycatch to ignore pathways with errors
- #105 Fixed relevel and added test_relevel.config
- #106 Fixed
--logFCthresholdbug - #108 Fixed blacklist file not working
- #88 Fixed volcano plot axis
- Bump versions to 1.3.2
- write deseq2 table to file
- Contrast names in report plots
- Convert species name to lower case also in report
- LogFC is also reported in the report and set in volcano plots
- Bump versions to 1.3.1
- Fix bug plots requested boxplots
- Bump versions to 1.3.0dev
- #74 Add option to provide KEGG pathway blacklist
- #74 Make quote param optional
- #74 Make report options optional (default in assets)
- #74 DE gene and pathway summary table
- #75 Boxplot of normalized counts can also be done from non-DE genes.
- #75 More comprehensive variable names and comments
- #74 Pathway analysis only perfomed if at least 2 DE genes
- Added report_options.yml in assets/.
- Skipping pathway analysis for contrasts with no found DE genes.
- Fixed report pvalue typo.
- Major changes in handling contrasts.
- Major improvements to report.
Initial pre-release of qbic-pipelines/rnadeseq, created with the nf-core template.