NGI-RNAseq v1.1

1.1 - 2017-05-23

New release of the pipeline with a few additions:

• Summary HTML report now created upon pipeline completion
  • This is saved in the results folder and also e-mailed if --email is set.
  • Nice way to alert the person running the pipeline that it completed and shows whether any errors were encountered.
  • Good for reproducibility as it logs all pipeline parameters to a easy to interpret file.
• Pipeline assumes that it's running with Paired-end files now
  • An error is now raised if the file glob doesn't give pairs of files
  • If running with single-end data, use the --singleEnd command-line option.
• Timelines and traces now created by default for the testing configs
• New configs and documentation about running the pipeline on AWS
• Made sure that the .bam files ended up in the main STAR directory when --saveAlignedIntermediates is used, instead of STAR/logs
• Made MultiQC load its config file through a channel instead of directly copying from baseDir