This repo is a modified fork of the original canu repo.

Important note

Note that the default branch of this repo is not master but v1.9_wdl_patch.

v1.9_wdl_patch is based on the v1.9 release of canu, and contains

• firstly re-formatting of the perl script canu.wdl and perl modules
• non-trivial adaptation of the perl code for friendliness to WDL and cloud (but does not contain any changes to the functional/C code)

• cherry-picked the following two commits—pushed after the v1.9 release—from the original/official canu repo fixing bugs in the meryl module:

  commit 82f608b4474fc8bd2d1416a1770f11c4e5348f9a
  Author: Brian P. Walenz <thebri@gmail.com>
  Date:   Wed Nov 13 16:17:50 2019 -0500
  
      Fix issue computing cutoff threshold when lots of noise kmers are present.  Issue #1538.
  
  commit 0fbbd0f6f070a01f2890540e44f02311dabd1e69
  Author: Brian P. Walenz <thebri@gmail.com>
  Date:   Wed Nov 13 16:17:13 2019 -0500
  
      Allow running with empty merylDB filename, for testing the threshold computation.  Issue #1538.
  

• expose an CLI to specify the value of $k$ (practically to allow $k = 31$) used in k-mer stats collection on parental reads.