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CHANGELOG.md

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cfDNA-Workflow Changelog

develop

  • general changes:

    • samples.schema.yaml
      • added optional info field for misc. info
      • added optional status field for sample status (e.g. disease status)

  • snakefile_WPS:

    • added dynamic .gz support
    • most intermediate files are .gz compressed

v0.3.2

  • Hotfix: fixed bug in get_refsample

  • update .gitignore

v0.3.1

  • Hotfix: unexpected behavior in conda environments

v0.3.0

  • updated documentation

  • comfort:

    • added geneIDs to WPS/COV/STARTs and FFT tables

  • snakefile_GE_analysis:

    • added background normalization
    • ported FFT calculation to python
    • separated multiple steps for increased maintainability

  • snakefile_WPS:

    • restructured file paths
    • moved window extension to separate
    • moved WPS padding correction to extractFromBAM_RegionBed_WPS_Cov.py

  • GE_unsupervised:

    • added rules for generating clusterings and heatmaps between all samples of an experiment using FFT intensities
      • kmeans clustering
      • HDBSCAN clustering
      • heatmaps
      • clustermaps (heatmap with hierarchical clustering)

v0.2.1

  • bugfix paths
  • simplified path handling in plotting scripts
  • improved readability of label files

v0.2.0

refactor

  • changed config.yml to example.config.yml
  • updated schemas
  • updated Documentation

new files

  • updated blacklists for both genome builds
  • updated genome files for both genome builds

new feature

  • snakefile_GE_analysis:

    • updated ProteinAtlas
      • 3 types: Blood, Tissue, Tissue+cell-lines
    • added support for GRCh38

  • snakefile_WPS:

    • added support for normalization by random background sequences
      • generate random background sequences not overlapping target regions
      • calculate WPS,COV,STARTS table for background sequences

  • extractFromBAM_RegionBed_WPS_Cov.py

    • added output for fragment endpoints (STARTS output)
    • added strand specificity

  • overlays.py:

    • integrated normalization by background sequences

v0.1.2

refactor

  • overlays.py
    • adding samples is now wrapped in a function
    • flanking regions are now determined dynamically

documentation

  • added README.md in config dir

  • updated README.md in root dir

    • updated input sections for workflows documentation
    • added links to .tsv files and README.md in config dir