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@Maarten-vd-Sande Maarten-vd-Sande released this 11 Dec 11:10
v0.6.0
ab9f440

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

Release 0.6.0 is a mix of bug fixes, small changes, and bigger stuff. Most importantly:

  • added a deseq2science command to do differential expression analysis on user-supplied tables with seq2science settings
  • for single-cell RNA-seq ADT-quantification is possible
  • snakemake library updated, giving seq2science a new-ish look :)

The full changes are listed below:

Added

  • added generic stats to the MultiQC report about the assembly, which might help pin point problems with the assembly used.
  • added the slop parameter to the config.yaml of atac-seq and chip-seq workflows, just so they are more visible.
  • added support for seurat object export and merging for kb workflow.
  • added support for CITE-seq-count for ADT quantification
  • added the option to downsample to a specific number of reads.
  • new deseq2science command

Changed

  • Seq2science now makes a separate blacklist file per blacklist option (encode & mitochondria), so that e.g. RNA-seq and ATAC-seq workflows can be run in parallel and don't conflict on the blacklist.
  • error messages don't show the full traceback anymore, making it (hopefully) more clear what is going wrong.
  • The effective genome size is now not calculated per sample, but per read length. When dealing with multiple samples (of similar) length this improves computational burden quite some.
  • samtools environment updated to version 1.14

Fixed

  • config option slop is now passed along to each rule using it
  • edge-case where local samples are in the cache, but not present in the fastq_dir
  • bug with differential peak/gene expression across multiple assemblies
  • bug with kb ref not creating index for non-velocity analysis
  • bug with count import in read_kb_counts.R for technical replicates and meta-data handling
  • deseq2 ordering in multiqc report
  • issue with slop not being used for the final count table
  • bug with onehot peaks not reporting the sample names as columns
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