Version 0.3

Version v0.3 of Cluster Flow. It's a big one!

Download

Download Cluster Flow v0.3 (.zip)
Download Cluster Flow v0.3 (.tar.gz)

Changelog

• New Stuff
  • Awesome new HTML report e-mails
    • Much more readable HTML report e-mails which look super-snazzy (see example)
    • Any errors are highlighted making them quick to identify (see example)
    • Custom strings set in the config can flagged as highlights or as warnings
    • Designed to work on desktop and mobile phone screens
  • Cluster Flow now re-orders the log file so that output from different modules doesn't overlap
    • Made each module prepend its stdout and sterr with a CF module flag
    • Made the cf_run_finished module parse the above flag and print out module by module
  • Rewrote how the environment module loading works - now much more robust
    • Uses modulecmd to prepare perl syntax commands
    • Moved code into the load_environment_modules function in Helpers.pm
  • Added environment module aliases
    • This allows you to load specific environment module versions or use different names to those specified within CF modules
    • eg. Replace fastqc with FastQC/0.11.2
• Updates
  • Made the bismark_methXtract module create genome-wide coverage reports if GTF path is available
  • Added the -q parameter to the FastQC module to make the log files cleaner
  • Removed the now uneccesary bismark_tidy module and renamed bismark_messy to bismark_report
• Bugs Squashed
  • Fixed dependency bug introduced in v0.2 which was making all downloads fire simultaneously
  • Fixed issue where modules using the CF::Constants Perl Module couldn't load the central config file
  • Fixed typo in environment module loading in bismark_align module
  • Reordered loading of the environment modules in trim_galore so that FastQC is loaded first, fixing dependency issues