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

Breaking change: Requires Snakemake >= v8.20.1

Full Changelog: v1.0.1...v2.0.0

v1.0.1 - stable version with complete docs and DOI

v1.0.1 - stable version with complete docs and DOI

Documentation

• Add Zenodo DOI

v1.0.0 - stable version with complete docs

Features

• Processing
  • (optional) Single-cell BAM file splitting into groups based on metadata.
  • Merging and indexing of BAM files by group.
  • Generation of bigWig files for merged BAM files.
  • Extraction and extension of gene coordinates from 12-column BED files.
  • Creation of a BED file for all genes and genomic regions for IGV-report.
• Visualization
  • Generation of customized plots for each gene/genomic region including all groups.
  • Creation of an interactive self-contained IGV-report for merged BAM files.
  • Setup of a UCSC genome browser track hub for all bigWigs, with color coding.

Documentation

• Usage Recommendations and advice for efficient workflow execution.
• Runtime information for ATAC-seq, RNA-seq, and scRNA-seq samples.
• Genome Browser Tracks: Instructions for using the UCSC Genome Browser Track Hub and IGV for visualization.
• Resources: Recommendations for compatible MR.PARETO modules and UCSC Genome Browser annotation track database

Full Changelog: v0.1.0...v1.0.0

v1.0.0 - stable version with complete docs

Features

• Processing
  • (optional) Single-cell BAM file splitting into groups based on metadata.
  • Merging and indexing of BAM files by group.
  • Generation of bigWig files for merged BAM files.
  • Extraction and extension of gene coordinates from 12-column BED files.
  • Creation of a BED file for all genes and genomic regions for IGV-report.
• Visualization
  • Generation of customized plots for each gene/genomic region including all groups.
  • Creation of an interactive self-contained IGV-report for merged BAM files.
  • Setup of a UCSC genome browser track hub for all bigWigs, with color coding.

Documentation

• Usage Recommendations and advice for efficient workflow execution.
• Runtime information for ATAC-seq, RNA-seq, and scRNA-seq samples.
• Genome Browser Tracks: Instructions for using the UCSC Genome Browser Track Hub and IGV for visualization.
• Resources: Recommendations for compatible MR.PARETO modules and UCSC Genome Browser annotation track database

Full Changelog: v0.1.0...v1.0.0

v0.1.0 - stable version with complete docs

A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.

features

• processing
  • BAM files of the same group are merged and indexed using samtools.
  • A bigWig file per merged BAM file is generated using deepTools::bamCoverage.
  • Information per requested gene from the 12-column BED file is retrieved (not necessary for genomic regions).
  • coordinates from the 12-column BED file are extracted and extended at the start and end by the configured parameter.
  • the number of isoforms i.e. number of lines in the BED file is determined (only for genes, for genomic regions it is hardcoded to 1) to plot below the tracks.
• visualization
  • generate one plot per category of bigWigs and gene/region with the determined gene parameters.
  • generate one plot including ALL categories per gene/region.

documentation

• complete documentation of used software, all features, and methods
• external resources