Release v0.3.0

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

Added

• fastp as aligner (default), makes trimgalore optional other aligner
• you can now specify an url for your samples file
• RNA-seq: gene_id to gene_name conversion table will be output for downstream analysis
  • (may be empty if gtf didn't contain both fields or wrong formatting)
• RNA-seq: quantifying with salmon will now also output a gene length table
  • (gene lengths, tpms and gene counts can still be found together in the SingleCellExperiment object)

Changed

• make use of pysradb for quering layout and SRR ids instead of API and web-scraping
• markduplicates now removes duplicates as default
• testing: clear genomepy caches between runs
• add parallel-fastq-dump fallback to fasterq-dump
• configuration rules split into more sections
• DESeq2 options renamed (from diffexp to deseq2 and contrasts)
• DESeq2 will now generate batch corrected counts (and TPMs for Salmon) for all samples, based on the set condition column.
  • (batch corrected output is still meant for downstream analysis that cannot model batch effects independently, e.g. plotting)

Fixed

• issue with control and technical replicates
• now also SRR numbers can be directly downloaded from ENA
• python3.8 syntaxwarnings
• chipseeker missing gtf input
• bugs with explain
• bwa-mem2 not working with less than 12 cores
• batch corrected TPMs no longer break when samples/rows are subset.