CARLISLE: Cut And Run anaLysIS pipeLinE

Bug fixes

• Bug fixes for DESeq (#127, @epehrsson)
  • Removes single-sample group check for DESeq.
  • Increases memory for DESeq.
  • Ensures control replicate number is an integer.
  • Fixes FDR cutoff misassigned to log2FC cutoff.
  • Fixes no_dedup variable names in library normalization scripts.
• Fig bug that added nonexistent directories to the singularity bind paths. (#135, @kelly-sovacool)
  • Containerize rules that require R (deseq, go_enrichment, and spikein_assessment) to fix installation issues with common R library path. (#129, @kelly-sovacool)
    • The Rlib_dir and Rpkg_config config options have been removed as they are no longer needed.

New features

• New visualizations: (#132, @epehrsson)
  • New rules cov_correlation, homer_enrich, combine_homer, count_peaks
  • Add peak caller to MACS2 peak xls filename
• New parameters in the config file to make certain rules optional: (#133, @kelly-sovacool)
  • GO enrichment is controlled by run_go_enrichment (default: false)
  • ROSE is controlled by run_rose (default: false)
• New --singcache argument to provide a singularity cache dir location. The singularity cache dir is automatically set inside /data/$USER/ or $WORKDIR/ if --singcache is not provided. (#143, @kelly-sovacool)

Misc

• The singularity version is no longer specified, per request of the biowulf admins. (#139, @kelly-sovacool)
• Minor documentation updates. (#146, @kelly-sovacool)