2.4 - A Pair of Shoes

Added

• #245 Added background gene list to pathway analysis output

Changed

• #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

Removed

• #247 Removed hard-coded comment about usage of gprofiler databases KEGG and REAC in the report

2.3 - Flowering Orchards

Added

• #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

Changed

• #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

Fixed

• #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

2.2 - Avenue of Poplars

Added

• #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 --quote parameter

Changed

• #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

Fixed

• #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

2.1 - Wheat Fields

Added

• #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

Changed

• #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

Fixed

• #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

Removed

• #150 Removed human and mouse db from env.yml, both are now installed during pipeline execution if needed

2.0.1 - Olive Trees hotfix I

Added

• #134 Corrected some versions
• #132 Bump version to 2.0.1
• #131 Added design_batcheffect.txt
• #130 Added test_batcheffect to github tests

Changed

• #131 Changed Sample_preparations.tsv by adding batch column

Fixed

• #130 Fixed batch effect bug

2.0 - Olive Trees

Added

• #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"

Changed

• #115 Template update
• #117 Turned LabID optional for report output in RNAseq_report.Rmd
• #110 Changed report to use rlog normalization by default, vst is used if --skip_rlog is enabled

Removed

• #108 Removed parameter "--report_options"
• #104 Removed functionality of parameter "--report_options", removed report_options.yml

Fixed

• #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 --logFCthreshold bug
• #108 Fixed blacklist file not working
• #88 Fixed volcano plot axis

1.3.2 - Almond blossom - Hotfix II

Fixed

• 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

1.3.1 Almond Blossoms hotfix

Added

• Bump versions to 1.3.1

Fixed

• Fix bug plots boxplots for requested genes

1.3.0 - Almond Blossoms

Added

• 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

Fixed

• #75 Boxplot of normalized counts can also be done from non-DE genes.
• #75 More comprehensive variable names and comments

Changed

• #74 Pathway analysis only perfomed if at least 2 DE genes

1.2.0 - starry night

• Fixed report pvalue typo
• Skipping pathway analysis for contrasts with no found DE genes
• Added report_options.yml in assets