qbic-pipelines/rnadeseq: 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 Removed assets/report_options.yml #110 Changed report to use rlog normalization by default, vst is used if --skip_rlog is enabled 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 #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 axi