v2.0.1 - Enable module usage using `github()` directive

• to enable module usage using github() directive
  • comment global.yaml (now requires full snakemake installation, not minimal)
• add nodefaults to all env YAML

Full Changelog: v2.0.0...v2.0.1

v2.0.0 - Snakemake 8 compatible & Duplicate handling

Breaking changes:

• Requires Snakemake >= v8.20.1
• Duplicate filtering with samtools view SAM flags and/or MACS2 during peak calling is now configurable.

Full Changelog: v1.1.0...v2.0.0

v1.1.0 - small enhancements and bug fixes

Enhancements

• TSS quantification was enhanced by providing BED file and annotation file for downstream analyses
• Promoter quantification was enhanced by providing an annotation file for downstream analyses

(Re)moved feature: bigWig Coverage & UCSC genome browser track hub generation

• removed all genome browser track/coverage/bigWig features in favor of the dedicated Genome Browser Track Visualization module

Bug fixes

• HOMER result aggregation fixed
• Limit promoter regions to chromosome size
• Exclude pseudoautosomal regions in human Y chromosome in promoter quantification

Documentation and rulegraph were updated accordingly.

Full Changelog: v1.0.1...v1.1.0

v1.0.1 - minor bug fixes

• fixed relative symlinks for MultiQC report creation
• handle the exception if HOMER returns no known motifs

Full Changelog: v1.0.0...v1.0.1

v1.0.0 - stable refactorized and enhanced version with complete docs and examples

Enhancements

• Refactorize pipeline, reduce scope/remove redundancy to dedicated downstream analysis modules, and integrate into MR.PARETO for v1.0.0.
• Abstract everything CeMM/BSF specific to the configuration level to make the pipeline more accessible.
• Revamp the MultiQC report to improve clarity and utility.
• Adapt result folder structure and reporting to conform with MR.PARETO standards.
• Simplify pipeline configuration to only two files (instead of 4) for ease of use.
• Ensure compatibility with Snakemake version 7.
• Implement quick aggregation of all quantifications, reducing processing time from mutliple hours to a few minutes.
• Make the slop_extension parameter configurable to accommodate different user needs.
• Aggregate sample-wise HOMER known motif enrichment results for easier downstream analysis.
• Add promoter and TSS region quantification features to the pipeline.
• Extract and present MultiQC statistics in a more accessible format.

Documentation

• Provide a tutorial and tips for quality control (QC).
• Add example microdata for human (hg38) and mouse (mm10) genomes to assist new users.
• Include a guide for resource downloading for required hg38 and mm10 data.
• Enable sharing of the genome browser track hub for collaborative work.
• Document the configuration process for UROPA within the pipeline.
• Point to downstream analysis modules.
• Adapt and extend Methods accordingly to refactorization, reduced scope and new features.

Small improvements

• Fix the mitochondrial fraction metric in the pipeline report.
• Create and add versioning to all environment YAML files.
• Make the installation of Homer a dedicated rule/job within the pipeline.
• Fix the multiqc.yaml installation error to ensure smooth setup.
• Remove temporary BAM files before Bowtie execution to save disk space and improve performance.
• Provide a consensus region annotation file, expanded by nucelotide content information.
• Clean up bash commands in all rules to improve code quality and maintainability.
• Split the UROPA region annotation rule to allow for parallel processing and increased efficiency.
• Tested the pipeline on 100 ATAC-seq samples as a loaded module within another Snakemake workflow project to ensure compatibility and robustness.

Full Changelog: v0.1.2...v1.0.0

v0.1.2 - add citation information

Full Changelog: v0.1.1...v0.1.2

v0.1.1 - transfer to epigen, updated and extended documentation

Full Changelog: v0.1.0...v0.1.1

the documentation was extended including

• a Methods template as a starting point for publications
• a list of used software and their respective publications (for proper referencing)
• minor improvements: Table of Contents, Authora, Resources...

v0.1.0 - first stable and internally used version

Full Changelog: https://github.com/sreichl/atacseq_pipeline/commits/v0.1.0