Cluster Flow v0.5

• Salmon - New module!
  • Written by @darogan
• Software versions now explicitly cleaned and printed to logs for all tools.
  • Final summary e-mails list versions at bottom.
  • New MultiQC module parses these, plus more.
• Launch logfile cf_[pipeline_id]_submissionlog.txt now lists environment information
  • Prints loaded environment modules, current PATH, user and system information
• Made use of $RealBin instead of $Bin
  • Cluster Flow now works when the main cf executable is symlinked
• Additional optional trimming parameters for TrimGalore! module
• Entirely new section of documentation describing module parameters
• Fixed a bug in parsing command line merge regexes.
• picard_dedup uses the environment TMPDIR if available
• Increased memory requirement for BWA alignment module.
• Many minor bugfixes