seq2science

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

• seq2science specific lockexception and cleanup metadata errors
• deseq2science now accepts the optional argument --assembly, which can be used if the samples.tsv contains >1 assembly to specify which one is used.
  • By default, the first assembly is used (same as before)

• rules that download something get re-tried once, in case internet is unstable
• bam files are no longer copied when sieving is not required
• moved blacklist rules to blacklist.smk
• rule inputs now use rules.rulename.output where possible
• renamed .smk files to match the naming schemes of the other .smks.
• added additional comments to clarify what happens to bam files
• cleanup cache+tarballs of conda environments, saving lots of precious disk space

• fixed custom assembly extensions (e.g. ERCC spike-ins) for scATAC-seq and scRNA-seq
• profiles work again
• deseq2science now has a clear separation between positional and optional arguments
• issue with blacklist bed containing more than 3 columns