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v0.9.0
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@kopardev kopardev released this 27 Apr 16:57
v0.9.0
855725a

Significant upgrades since the last release:

  • updates to wrapper script, many new arguments/options added
  • new per-sample counts table format
  • new all-sample master counts matrix with min-nreads filtering and ntools column to show number of tools supporting the circRNA call
  • new version of Snakemake
  • cluster_status script added for forced completion of pipeline upon TIMEOUTs
  • updated flowchart from lucid charts
  • added circRNAfinder, find_circ, circExplorer2_bwa and other tools
  • optimized execution and resource requirements
  • updated viral annotations (Thanks Sara!)
  • new method to extract linear counts, create linear BAMs using circExplorer2 outputs
  • new job reporting using jobby and its derivatives
  • separated creation of BWA and BOWTIE2 index from creation of STAR index to speed things up
  • parallelized find_circ
  • better cleanup (eg. deleting _STARgenome folders, etc.) for much smaller digital footprint
  • multitude of comments throughout the snakefiles including listing of output file column descriptions
  • preliminary GH actions added
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