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v1.13-RC.1

Alexis Mergez requested to merge dev into main

v1.13-RC.1

  • Added Pan1c_View report tarball
  • Added Minigraph-Cactus as gtool to generate graphs (with/instead of PGGB)
  • Documented rules
  • Running Assemblathon_stats.pl by default to compute stats on input assemblies
  • Removed usage of pggb.sif for PanGeTools.sif
  • Added vg deconstruct option (get_VCF)
  • Removed PAV option from config.yaml (script still exists but is untested)
  • Updated getApps.sh
  • Added cluster execution script (runSnakemakeSLURM.sh) and instructions
  • Reduced constraints on chromosome names (everything allowed now, previously required chr prefix)
  • Updated README

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