nf-core/rnaseq: nf-core/rnaseq version 1.0

Initial release of nf-core/rnaseq! This release marks the point where the pipeline was moved from SciLifeLab/NGI-RNAseq over to the new nf-core community, at nf-core/rnaseq. You can view the previous changelog at SciLifeLab/NGI-RNAseq/CHANGELOG.md In addition to porting to the new nf-core community, the pipeline has had a number of major changes in this version. There have been 157 commits by 16 different contributors covering 70 different files in the pipeline: 7,357 additions and 8,236 deletions! In summary, the main changes are: Rebranding and renaming throughout the pipeline to nf-core Updating many parts of the pipeline config and style to meet nf-core standards Support for GFF files in addition to GTF files Just use --gff instead of --gtf when specifying a file path New command line options to skip various quality control steps More safety checks when launching a pipeline Several new sanity checks - for example, that the specified reference genome exists Improved performance with memory usage (especially STAR and Picard) New BigWig file outputs for plotting coverage across the genome Refactored gene body coverage calculation, now much faster and using much less memory Bugfixes in the MultiQC process to avoid edge cases where it wouldn't run MultiQC report now automatically attached to the email sent when the pipeline completes New testing method, with data on GitHub Now run pipeline with -profile test instead of using bash scripts Rewritten continuous integration tests with Travis CI New explicit support for Singularity containers Improved MultiQC support for DupRadar and featureCounts Now works for all users instead of just NGI Stockholm New configuration for use on AWS batch Updated config syntax to support latest versions of Nextflow Built-in support for a number of new local HPC systems CCGA, GIS, UCT HEX, updates to UPPMAX, CFC, BINAC, Hebbe, c3se Slightly improved documentation (more updates to come) Updated software packages ...and many more minor tweaks. Thanks to everyone who has worked on this release