Version 2.2.5

• Add homer motif calling to differential peaksets and CHiP whole peak sets

Version 2.2.4

Update and fix cut & run cli

Version 2.2.3

• Fix problems with multiqc pulling in enhancer plot
• Fix file path issue with deeptools_gene_all
• Updated annotations for hg38 and mm10

Version 2.2.2

• chore: moved FRiP and jaccard rules to peakqc.smk
• fix: bug in FRiP_SEACR rule
• docs: improved documentation regarding blocking

Version 2.2.1

• verification of auto release from fork

Version 2.2.0

MultiQC report revamp

• Update of multiQC version used to v1.32 via sif container
• Complete recreation of the multiQC yaml in references (changes include splitting modules, changing flow, and adding manual descriptions)
• Addition to multiQC report of: Encode QC metrics, interactive enhancer profile plots (when created), interactive Spearman correlation plot, interactive TSS profile plots
• Also includes a minor bug fix so that DiffBind_QC rules do not rerun every run of the pipeline

Continuous Integration

• Adding multiple CI components to harden pipeline
  • check version
  • auto release
  • snakevis on release

v2.1.0

What's Changed

• feat: Adding new summary tables of QC stats by @rroutsong in #100
• feat: Adding mm39 reference genome by @rroutsong @tovahmarkowitz in #102
• docs: Adding docs for manually running DiffBind outside of pipeline by @rroutsong @tovahmarkowitz in #94
• fix: Bug fixes by @rroutsong in #103 #104 #105

Full Changelog: v2.0.0...v2.1.0

v2.0.0

What's Changed

New features:

• FRiP plotting
• DiffBindQC report (DiffBind-based peak calling comparison across samples)
• TPM counts of consensus peaks for external differential peak calling
• Deeptools plots: spearman correlation, pearson correlation, PCA, fingerprint plot,
  metagene plots, TSS plots, enhancer plots
• Addition of the cutnrun assay with SEACR
• Homer for motif calling
• Jaccard calculation
• Merged table of differential peak table and uropa finalhits output

Improvements

• DiffBind differential peak calling reorganization and improved html reports
• Separation of PE and SE rules
• Encode QC metric calculation on PE data without requirement of ppqt
• Improved documentation
• Improvements to peakcall file parsing and new column names
• Addition of peakcall file highlighting to make error checking easier
• Expanded rerun triggers

Full Changelog: v1.2.0...v2.0.0

v1.2.0

What's Changed

• Major refactor codebase by @rroutsong in #41
• Added time stamp to slurm out and err logs by @rroutsong in #42
• Removal of MEME and SICER due to issues in the previous version
• UROPA now only runs protTSS option

New Contributors

• @rroutsong Made their first contribution 🎉 in #41

Full Changelog: v1.1.0...v1.2.0

v1.1.0

What's Changed

• Update Snakefile by @tovahmarkowitz in #30
• add blocking to the diffbind csv prep by @tovahmarkowitz in #35
• Adding new DiffBind QC Rmd for cfChIP and a few other DiffBind updates by @tovahmarkowitz in #36
• Adding new DiffBindQC for cfChIP by @tovahmarkowitz in #37
• Adding memory for diffbind jobs by @tovahmarkowitz in #38
• Updates to CI include every major permutation of running the ChIP-, cfChIP-, and ATAC-seq pipelines @skchronicles
• Updates to documentation to include FAQ and description/overview of pipeline and its different types of output files @tovahmarkowitz @skchronicles
• Re-building cfChIP docker image to include additional R packages @skchronicles
• Adding MEME to pipeline @tovahmarkowitz
• Adding spearman heatmap and PCA plots @tovahmarkowitz
• Updates to handle single-end data @tovahmarkowitz
• Updates to handle ChIP-seq data/processing lacking input control samples @tovahmarkowitz

Full Changelog: v1.0.2...v1.1.0