NGI-RNAseq v1.3

• Updated HISAT2 from v2.0.5 to v2.1.0
  • Uses --new-summary and --summary-file to give output that will work with MultiQC,
  • UPPMAX environment module load and Docker image
• Moved pipefail statement into config, applies to all processes
• Rewrote summary e-mail commands. Now uses sendmail
  • Proper multipart text/html e-mail with embedded images
  • If sendmail fails, falls back to sending plaintext using mail
• MultiQC process now runs using local executor for internet access on some UPPMAX clusters.
• UPPMAX featureCounts process now loads python/2.7.11 environment module
• New test script for uppmax with HISAT2
• Timeline and trace now always generated for every run
• Script now checks that the version of Nextflow is recent enough and warns if not
• New --help function to give usage help
• Software versions are now collected at run time and added to MultiQC and pipeline reports.
• RSeQC has been refactored, and geneBody_coverage.py moved into it's own process.
• The way config files work has been changed. Config settings are now inherited from base.config instead of uppmax.config
  • igenome.config needs to be last in the profile definition for the inhertence to work properly