html output option not available in v 0.3.3?

[caonetto]

Hi, How can we generate the html report ouput that used to be available using the -o option in histgrowth?

Cheers.

[danydoerr]

It's still available, but we moved it into a separate command panacus report where you specify a yaml config for the calculations that you want panacus to perform.

Here's an example

- !Growth
  name: testing this
  count_type: Bp
  graph: /path/to/graph.gfa

[heringerp]

To generate an HTML report, you can use the report command as: panacus report <YAML_CONFIG_FILE>. For this you need a file containing the configuration for the HTML report you want to generate. An example for such a file could be:

- !Hist
  name: test_hist
  count_type: Bp
  graph: ../graphs/test.gfa
- !Growth
  hist: test_hist
  coverage: 1,1,2
  quorum: 0.1,1,0.1

This will create a report containing the coverage histogram and growth curve for the graph ../graphs/test.gfa. Each section corresponds to one possible analysis. Below it the parameters for that analysis are specified. You can find a list of all the possible parameters/sections here: https://github.com/marschall-lab/panacus/wiki/YAML-report-file

[caonetto]

Thank you for your quick response!