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Release v0.5.1

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@Maarten-vd-Sande Maarten-vd-Sande released this 01 Apr 17:46
v0.5.1
ca8ccb1

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

Added

  • added CLI functionality to the deseq2.R script (try it with Rscript /path/to/deseq2.R --help!)
  • --force flag to seq2science init to automatically overwrite existing samples.tsv and config.yaml
  • local fastqs with Illumina's '_100' are now recognized
  • added the workflow explanation to the multiqc report

Changed

  • config checks: all keys converted to lower case & duplicate keys throw an exception
  • MultiQC updated to v1.10
  • Link to seq2science log instead of snakemake log in final message

Fixed

  • Issue when filtering a combination of single-end and paired-end reads on template length
  • explain functionality testing
  • scATAC can properly use SE fastqs
  • scRNA can use fqexts other than R1/R2
  • fastq renaming works again
  • added missing schemas to extended docs

Fixed

  • Bug with edgeR.upperquartile normalization. Now makes everything NaN, so pipeline finishes succesfully.
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