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TODO.md

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TODO

  1. Implement jobs by rounds instead of strict post-order traversal of intput tree Completed 4.25.2022
  2. Add resource options to config Completed 8.4.2022
  3. halAppend steps Completed 7.7.2022
  4. Test various issues (e.g. the --restart flag, --configFile) Completed 8.4.2022
  5. Add a rule to copy the final HAL file before appending the other HALs to it so it that step doesn't have to be re-done if the later steps need to be re-run Completed 8.4.2022
  6. Add a rule to convert the final HAL to MAF Defunct 8.24.2022, this will be done with Comparative Augustus
  7. Add a non-gpu option for the mask and blast rules Completed 8.24.2022
  8. Update to cactus 2.2.0 Completed 8.24.2022
  9. Add in a workflow to add a genome to an alignment (https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/cactus-update-prepare.md)