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Release v0.2.0
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@Maarten-vd-Sande Maarten-vd-Sande released this 04 Aug 09:10
v0.2.0
15c04f9

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

Fixed

  • Allow for same condition name across different assemblies & different controls

Added

  • HISAT2 as aligner for RNA-seq
  • splice-aware HISAT2 indexing for RNA-seq
  • quantifier HTSeq for RNA-seq
  • quantifier featurecounts for RNA-seq
  • Salmon will output a gene-level TPM matrix as well
  • added/expanded seq2science explain info (now covers RNA- and scATAC-seq too)
  • sequencing strandedness may now be inferred automatically (unless specified in the config/samples.tsv)
  • strandedness results are displayed in the multiQC under "Strandedness"
  • a DEXSeq counts matrixs can now be generated with dexseq: True
  • seq2science CLI now has the same reason flag as snakemake (-r/--reason flag)
  • (re)added fnwi + rimls logos to the qc reports that went missing in seq2science migration

Changed

  • rules and script names in RNA-seq. ex: txi.R is now quant_to_counts.R to better reflect its function
  • quant_to_counts.R now converts salmon transcript abundances to gene counts identically to DESeq2
  • STAR no longer outputs counts, and is no longer found under quantifiers
  • gene counts are generated from (filtered) bams when using either STAR or HISAT2 as aligner and HTSeq or featureCounts are quantifier
  • batch corrected gene counts are generated if a DESeq2 design contrast inclused a batch
  • batch corrected TPM are generated if a DESeq2 design contrast inclused a batch, and quantification was performed using Salmon
    • for us in ANANSE, for instance
  • seq2science explain now retrieves messages from explain.smk.
  • seq2science explain now used profiles and snakemakeOptions.

Fixed

  • the alignment workflow no longer uses strandedness
  • seq2science CLI can now be run without cores with a dryrun or profile with cores
  • Jenkins code style (now used mamba to install flake8)
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