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@Ulthran Ulthran released this 08 Aug 15:43
v4.0.0
023f343

Release of Sunbeam version 4! This version includes the outsourcing of many non-essential parts of the pipeline to optional extensions, integration of snakemake profiles to simplify the command line and make interactions with various cluster/cloud management systems easier, a new and improved testing suite (written with PyTest), and various bug fixes and QoL improvements.

  • Many components of sunbeam have been moved extensions to minimize installation and usage issues with the core pipeline, qc and decontam are the remaining core components
  • Deprecated --cluster-config snakemake option replaced with profiles, also reduces sunbeam's command line interface by moving options to the profile
  • Improved logging and reporting standards for sunbeam and extensions
  • Restructured to snakemake standards for tarball installation methods
  • Switch test suite from bash to pytest to increase ease and efficiency of testing
  • Updated documentation
  • Fixed minor bugs in sunbeam config modify
  • Added cutadapt options to sunbeam config
  • Catch empty fastqc reports that would otherwise error out
  • Replace os.system calls with subprocess
  • Use unmapped reads directly from samtools instead of previous method of filtering them manually
  • Remove rbt and biopython, rewriting functions manually instead of using heavy dependencies
  • Improving filter_reads efficiency on large hostid sets and catching errors in sequence header matching
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