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@Maarten-vd-Sande Maarten-vd-Sande released this 21 Apr 08:31
v0.9.9
6ae4c6a

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows.

[0.9.9] - 2023-04-21

Changed

  • moved downloading fastqs to localrules
  • bam indexes are kept (not automatically removed)
  • Salmon updated to the latest version v1.10.1 (fixes a bug)
  • upsetplot updated to the latest version (fixes a bug)
  • genomepy updated to the latest version (no reason)
  • tabulate updated to the latest version (longer python support)
  • everything else updated to the latest version
  • --snakemakeOption debug_dag=True can now be used with 1 core (required)
  • creating conda environments now faster
    • updated conda & mamba
    • dropped indexing of Conda's defaults channel
  • one less global variable! (sanitized_samples)
  • dropped correlation scores from DESeq2 clusterplots
    • pheatmap is too finickey to get the fontsize right
  • pheatmap uses the sample order (from the samples.tsv) as best as possible

Fixed

  • edge case when a GSM sample is a reanalysis of another GSM sample.
  • error message referring to --config while it should be --configfile
  • cyclic dependency on rule samtools_sort (caused by tildes in config paths)
  • bug in DESeq2 related rules when using custom assemblies
  • clear error message when downloading single-end data annotated as paired-end.
  • "Max retries exceeded with url" for CRX samples
  • upsetplot & assembly_stats segfault due to interactive matplotlib backend
  • DESeq2 error: "EOF within quoted string"
  • conda environment channel priorities
  • trackhub index generation now removes rogue spaces from the annotation (instead of crashing)
Assets 2
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