Release 2.0 - Olive Trees · qbic-pipelines/rnadeseq

#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
#110 Changed report to use rlog normalization by default, vst is used if --skip_rlog is enabled

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

#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

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