Skip to content

Releases: qbic-pipelines/rnadeseq

2.4 - A Pair of Shoes

23 Jul 10:35
ffbf84a
Compare
Choose a tag to compare

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

17 Jun 13:02
163c7ee
Compare
Choose a tag to compare

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

21 Aug 08:44
f5e54b6
Compare
Choose a tag to compare

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

31 Jan 12:36
64f7f63
Compare
Choose a tag to compare

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

23 Jun 09:17
c75cf36
Compare
Choose a tag to compare

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

02 Jun 09:23
789b138
Compare
Choose a tag to compare

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

09 Oct 06:51
abe7427
Compare
Choose a tag to compare

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

30 Sep 15:31
7d3a1e7
Compare
Choose a tag to compare

Added

  • Bump versions to 1.3.1

Fixed

  • Fix bug plots boxplots for requested genes

1.3.0 - Almond Blossoms

29 Sep 12:45
20700da
Compare
Choose a tag to compare

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

11 Sep 10:41
e9350d2
Compare
Choose a tag to compare
  • Fixed report pvalue typo
  • Skipping pathway analysis for contrasts with no found DE genes
  • Added report_options.yml in assets