This repo is a modified fork of the original canu repo.
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
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firstly re-formatting of the perl script
canu.wdland 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)
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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.