Optionally ignore errors

[bschiffthaler]

Suggesting this as a quick fix for issues that arise during report generation. Examples can be found here:

#309
#295
#221
#219

This adds a flag --ignore-report-errors to the qc python script which sets knitr::opts_chunk$set(error = TRUE) Rmd for the html report and sets options(error = function() {}) for the process in general.

[Fabian-RY]

Hi @bs-az I've seen the changes are interesting, especially some things that I didn't notice (like having the echo twice in the .Rmd report file).

I'm currently working in solving these issues, so plots that fail to be generated, and that now make the report fail, are:

• Either not shown, because they are pointless if they have no value (For example, those that show data only of FSM, if there are no FSMs)
• The value they should show was zero and, as is, the plots show nothing, but it would be missed info that is important

I'm currently testing my changes, that affect directly SQANTI3_report.R, recently pushed to a testing branch. With this changes, there's no need to ignore the errors via a command line argument, as it will handle correctly the empty data that causes it to fail.

Anyway, I want to thank you for your contribution.