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Recent Releases of atacseq_pipeline

atacseq_pipeline - v2.1.0 - Sample annotation visualization for QC

Full Changelog: https://github.com/epigen/atacseq_pipeline/compare/v2.0.2...v2.1.0

- Python
Published by sreichl 8 months ago

atacseq_pipeline - v2.0.2 - Minor fixes

  • make all resource files input to rules

Full Changelog: https://github.com/epigen/atacseq_pipeline/compare/v2.0.1...v2.0.2

- Python
Published by sreichl 9 months ago

atacseq_pipeline - 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: https://github.com/epigen/atacseq_pipeline/compare/v2.0.0...v2.0.1

- Python
Published by sreichl about 1 year ago

atacseq_pipeline - 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: https://github.com/epigen/atacseq_pipeline/compare/v1.1.0...v2.0.0

- Python
Published by sreichl over 1 year ago

atacseq_pipeline - 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

Bug fixes

Documentation and rulegraph were updated accordingly.

Full Changelog: https://github.com/epigen/atacseq_pipeline/compare/v1.0.1...v1.1.0

- Python
Published by sreichl almost 2 years ago

atacseq_pipeline - v1.0.1 - minor bug fixes

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

Full Changelog: https://github.com/epigen/atacseq_pipeline/compare/v1.0.0...v1.0.1

- Python
Published by sreichl about 2 years ago

atacseq_pipeline - 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: https://github.com/epigen/atacseq_pipeline/compare/v0.1.2...v1.0.0

- Python
Published by sreichl about 2 years ago

atacseq_pipeline - v0.1.2 - add citation information

Full Changelog: https://github.com/epigen/atacseq_pipeline/compare/v0.1.1...v0.1.2

- Python
Published by sreichl almost 3 years ago

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

Full Changelog: https://github.com/epigen/atacseq_pipeline/compare/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...

- Python
Published by sreichl almost 4 years ago

atacseq_pipeline - v0.1.0 - first stable and internally used version

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

- Python
Published by sreichl almost 4 years ago