• Fix how singularity bind paths are set. (#187, @kelly-sovacool)
• Fix the DESeq rule when using the hs1 T2T genome. (#187, @kelly-sovacool, @wong-nw)
• Fix incorrect jobby version (needs v0.4). (#194, @kelly-sovacool)
• Fix jobby usage to output stdout/stderr to log file. (#196, @kopardev)
• Fix numpy error. (#198, @kelly-sovacool)
• Fix logic error with scaling factor calcutions. (#195, @kopardev)
• Run MACS2 with control by default. (#195, @kopardev)
• Make sure submit_slurm.sbatch is not overwritten. (#195, @kopardev)
• Handle case when sample names are subsets of each other. (#195, @kopardev)

• Remove deprecated 'ccr' partition. (#176, @kopardev)

• Now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#168, @kelly-sovacool)

• Fix driver script: do not try to load the shared conda environment. (#166, @kelly-sovacool)

• Minor documentation update to use readthedocs theme. (#162, @kelly-sovacool)
• Fix deprecation warning during initialization. (#163, @kelly-sovacool)

• Documentation improvements. (#154, @kelly-sovacool)
• If jobby & spooker are not available, try adding them to the path on workflow completion. (#155, @kelly-sovacool)
• Fix bug that flipped library normalization scaling factor (#157, @epehrsson)

• Load the module for snakemake v7, but do not specify the minor and patch versions. (#149, @kelly-sovacool)

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)

What's Changed

• Citation updates by @kelly-sovacool in #111
• Adds a --force flag to allow for re-initialization of a workdir @slsevilla, #97
• Fixes error with testrun in DESEQ2 @slsevilla, #113
• Decreases the number of samples being run with testrun, essentially running tinytest as default and removing tinytest as an option @slsevilla, #115
• Reads version from VERSION file instead of github repo link @slsevilla, #96 and #112
• Added a CHANGELOG @slsevilla, #116
• Refactor R library handling @slsevilla, #117
• Adds missing mm10 parameters @slsevilla, #121
• Removes some testing from annotation report gopeaks due to latency @slsevilla, #125

Full Changelog: v2.4.1...v.2.5.0

What's Changed

• Add GitHub Action to add issues/PRs to personal project boards by @kelly-sovacool in #95
• Create install script by @kelly-sovacool in #93
• feat: use summits bed for homer input; save temporary files; fix deseq2 bug by @slsevilla in #108
• docs: adding citation and DOI to pipeline by @slsevilla in #107
• Test a dryrun with GitHub Actions by @kelly-sovacool in #94
• version 2.4.1 updates by @slsevilla in #110

New Contributors

• @kelly-sovacool made their first contribution in #95

Full Changelog: v2.4.0...v2.4.1