2.6.3

This release add job scheduling support, improves assembly error debugging, and bug fixes.

• Added support for distributing assembly work across multiple nodes
  • Use the --jobindex and --jobnodes nodes parameters to distribute the work
  • Added examples/torque_example.sh
• Fatal assembly errors now generate a zip file containing the minimal data required to reproduce the issue. This file includes the following:
  • input file metrics
  • reads in the assembly graph at time of failure
  • reference genome. All regions not relevant to the failure are masked (replaced with N)
  • configuration file (if used)

Bug fixes/minor enhancements:

• Fixed assembly error (#260)
• Added checks to ensure assembly and variant calling have same inputs (#261)
• cohort scripts updated to match driver script (#240)
• SoftClipToSplitReads now writes temporary files to the correct directory (#250)
• Forcing C locale to prevent locale-based parsing errors due to number formatting (#253)
• Downgraded getopt failure to warning (#251)
• Added --picardoptions to expose standard command line options (#254)
  • Useful options include VALIDATION_STRINGENCY=LENIENT and COMPRESSION_LEVEL=0. See https://broadinstitute.github.io/picard/command-line-overview.html
• Removed PON generation script as it's been replaced by gridss.GeneratePonBedpe
• Fixed SoftClipToSplitReads duplicating SAM headers when using external merge
• Made terminal sambamba steps idempotent (#255)
• Exposing assembly read name prefix in assembly.contigNamePrefix configuration file parameter (#182, #261)
• Forcing assembly reinitialisation when unsupported assembly encountered