Closed syansanofi closed 3 years ago
@syansanofi Hi Shu,
Do I understand correctly that the --amplicons
argument should also be removed from the template along with other parameters?
@syansanofi Hi Shu, Do I understand correctly that the
--amplicons
argument should also be removed from the template along with other parameters?
Yes! We can remove it
Issue
Novoalign version 4 has new tune features that are sets of parameters specifically tested against data from individual sequencers such as Novaseq, Hiseq...etc. These features are available in --tune. Defaults without tuning has been updated as well.
Approach
Remove all aligner parameters and replace with tune. The tune parameter is optional so by default, command should have no
--tune
.https://github.com/epam/fonda/blob/9322c5f7ddf34e7c4068b788c52c8599337f4202/src/main/resources/templates/novoalign_sort_tool_template.txt#L2
should become something similar to the following:
For integration purposes, here are the
--tune
options and what other parameters are set to for each one. Column headers denote the option string.Source: http://www.novocraft.com/downloads/V4.00.Pre-20190805/NovoalignVersion4.pdf