seq2science

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

• renamed most globals in uppercase (main exceptions are config and samples, treps and breps)
• moved most configuration steps into functions (reducing the number of stray globals)
• replaced static functions with dictionaries
• moved replicate stuff to the configuration
• Updated Salmon
• Added the option for Salmon to use the full genome as decoy sequence
• Salmon now uses the full genome as decoy sequence by default.
  • Config option quantifier_decoys controls which level of decoy aware quantification you want (options are 'none', 'partial' and 'full')
  • Option 'partial' is insanely memory intensive, and the Salmon docs suggest no benefit...
• improved parsing of the samples.tsv. More errors early on, to prevent headache later!

• get_fastq_pair_reads() was using one sample, not any sample
• error message not working when trimming in scRNA-seq
• trackhubs when using a mix of stranded and unstranded datasets
• fix samples.tsv checks for forbidden symbols