v1.2.2

1.2.2 (2026-07-30)

Documentation

• point container instructions at the published Apptainer image (57dd6d1)

v1.2.1

1.2.1 (2026-07-30)

Documentation

• regenerate tube map with the diffopen + footprinting stages (f4d988a)

v1.2.0

1.2.0 (2026-07-30)

Added

• replace DESeq2 notebook with integrated diffopen stage + add apptainer.def (9c11142)

v1.1.1

1.1.1 (2026-07-15)

Documentation

• restructure README usage-first and fold footprinting into the workflow tube map (1d9489a)

v1.1.0

[1.1.0] - 2026-07-14

Added

• Optional TOBIAS TF-footprinting stage (footprint_all target,
  workflow/rules/footprint.smk): pools replicate BAMs per condition (from the
  sample sheet's type column), removes Tn5 insertion bias (ATACorrect),
  scores footprints (ScoreBigwig), and reports differential TF binding across
  conditions from JASPAR motifs (BINDetect). Opt-in — not part of the default
  run. Adds the jaspar_motifs config key and the tobias conda environment.

Fixed

• The QC RPGC bedgraph (deeptools_bedgraph) now excludes blacklist regions
  (--blackListFileName), matching the primary create_bigwig coverage track.

Full Changelog: v1.0.0...v1.1.0

v1.0.0

First release: an ATAC-seq Snakemake workflow with RPGC depth-normalized
coverage (no spike-in). Adapted from the spike-in–normalized sibling workflow
by dropping spike-in alignment/normalization and using read-depth normalization.

Primary stage (atacseq_all): FastQC/fastp → Bowtie2 alignment to a human
index → filtering/dedup/blacklist → MACS2 peaks → RPGC depth-normalized bigWigs
→ reproducible fixed-width consensus peaks + featureCounts matrix.

QC stage (qc_all): deepTools QC, FRiP, IDR, library complexity, TSS
enrichment, reads-in-annotation, and a self-contained interactive HTML QC report.

Differential analysis (ATACseq_Dx.ipynb): DESeq2 (median-of-ratios)
differential binding on the consensus counts (promoter vs distal, paired design)
plus Gviz browser tracks from the RPGC bigWigs.

Full Changelog: https://github.com/gynecoloji/snakemake_ATACseq/commits/v1.0.0