qbic-pipelines/rnadeseq: 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 to 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 repor