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CHANGELOG.md

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CARLISLE development version

CARLISLE 2.6.1

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

CARLISLE 2.6.0

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)

CARLISLE v2.5.0

  • Refactors R packages to a common source location (#118, @slsevilla)
  • Adds a --force flag to allow for re-initialization of a workdir (#97, @slsevilla)
  • Fixes error with testrun in DESEQ2 (#113, @slsevilla)
  • Decreases the number of samples being run with testrun, essentially running tinytest as default and removing tinytest as an option (#115, @slsevilla)
  • Reads version from VERSION file instead of github repo link (#96, #112, @slsevilla)
  • Added a CHANGELOG (#116, @slsevilla)
  • Fix: RNA report bug, caused by hard-coding of PC1-3, when only PC1-2 were generated (#104, @slsevilla)
  • Minor documentation improvements. (#100, @kelly-sovacool)
  • Fix: allow printing the version or help message even if singularity is not in the path. (#110, @kelly-sovacool)

CARLISLE v2.4.1

  • 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

CARLISLE v2.4.0

  • Feature- Merged Yue's fork, adding DEEPTOOLS by @slsevilla in #85
  • Feature- Added tracking features from SPOOK by @slsevilla in #88
  • Feature - Dev test run completed by @slsevilla in #89
  • Bug - Fixed bugs related to Biowulf transition

CARLISLE v2.1.0

  • enhancement
  • update gopeaks resources
  • change SEACR to run "norm" without spikein controls, "non" with spikein controls
  • update docs for changes; provide extra troubleshooting guidance
  • fix GoEnrich bug for failed plots

CARLISLE v2.0.1

  • fix error when contrasts set to "N"
  • adjust goenrich resources to be more efficient

CARLISLE 2.0.0

  • Add a MAPQ filter to samtools (rule align)
  • Add GoPeaks MultiQC module
  • Allow for library normalization to occur during first pass
  • Add --broad-cutoff to MACS2 broad peak calling for MACS2
  • Create a spike in QC report
  • Reorganize file structure to help with qthreshold folder
  • Update variable names of all peak caller
  • Merge rules with input/output/wildcard congruency
  • Convert the "spiked" variable to "norm_method
  • Add name of control used to MACS2 peaks
  • Running extra control:sample comparisons that are not needed
  • improved resource allocation
  • test data originally included 1475 jobs, this version includes 1087 jobs (reduction of 25%) despite including additional features
  • moved ~12% of all jobs to local deployment (within SLURM submission)

CARLISLE 1.2.0

  • merge increases to resources; update workflow img, contributions

CARLISLE 1.1.1

  • patch for gz bigbed bug

CARLISLE 1.1.0

  • add broad-cutoff to macs2 broad peaks param settings
  • add non.stringent and non.relaxed to annotation options
  • merge DESEQ and DESEQ2 rules together
  • identify some files as temp

CARLISLE 1.0.1

  • contains patch for DESEQ error with non hs1 reference samples