Major novel changes include: Support for Salmon as an alternative method to STAR and HISAT2 Several improvements in featureCounts handling of types other than exon. It is possible now to handle nuclearRNAseq data. Nuclear RNA has un-spliced RNA, and the whole transcript, including the introns, needs to be counted, e.g. by specifying --fc_count_type transcript. Support for outputting unaligned data to results folders. Added options to skip several steps Skip trimming using --skipTrimming Skip BiotypeQC using --skipBiotypeQC Skip Alignment using --skipAlignment to only use pseudo-alignment using Salmon Documentation updates Adjust wording of skipped samples in pipeline output Fixed link to guidelines #203 Add Citation and Quick Start section to README.md Add in Documentation of the --gff parameter Reporting Updates Generate MultiQC plots in the results directory #200 Get MultiQC to save plots as standalone files Get MultiQC to write out the software versions in a .csv file #185 Use file instead of new File to create pipeline_report.{html,txt} files, and properly create subfolders Pipeline enhancements & fixes Restore SummarizedExperimment object creation in the salmon_merge process avoiding increasing memory with sample size. Fix sample names in feature counts and dupRadar to remove suffixes added in other processes Removed genebody_coverage process #195 Implemented Pearsons correlation instead of Euclidean distance #146 Add --stringTieIgnoreGTF parameter #206 Removed unused stringtie channels for MultiQC Integrate changes in nf-core/tools v1.6 template which resolved #90 Moved process convertGFFtoGTF before makeSTARindex #215 Change all boolean parameters from snake_case to camelCase and vice versa for value parameters Add SM ReadGroup info for QualiMap compatibility#238 Obtain edgeR + dupRadar version information #198 and #112 Add --gencode option for compatibility of Salmon and featureCounts biotypes with GENCODE gene annotations Added functionality to accept compressed reference data in the pipeline Check that gtf features are on chromosomes that exist in the genome fasta file #274 Maintain all gff features upon gtf conversion (keeps gene_biotype or gene_type to make featureCounts happy) Add SortMeRNA as an optional step to allow rRNA removal #280 Minimal adjustment of memory and CPU constraints for clusters with locked memory / CPU relation Cleaned up usage, parameters.settings.json and the nextflow.config Dependency Updates Dependency list is now sorted appropriately Force matplotlib=3.0.3 Updated Packages Picard 2.20.0 -> 2.21.1 bioconductor-dupradar 1.12.1 -> 1.14.0 bioconductor-edger 3.24.3 -> 3.26.5 gffread 0.9.12 -> 0.11.4 trim-galore 0.6.1 -> 0.6.4 gffread 0.9.12 -> 0.11.4 rseqc 3.0.0 -> 3.0.1 R-Base 3.5 -> 3.6.1 Added / Removed Packages Dropped CSVtk in favor of Unix's simple cut and paste utilities Added Salmon 0.14.2 Added TXIMeta 1.2.2 Added SummarizedExperiment 1.14.0 Added SortMeRNA 2.1b Add tximport and summarizedexperiment dependency #171 Add Qualimap dependency #202