capture and report DenovoAssemblyError at trinity step

[dpark01]

We recently introduced a DenovoAssemblyError in the assemble_trinity step that makes trinity failures more interpretable. Similar to what is done for PoorAssemblyError currently, can this error be captured and logged in a more user friendly way? This would then obviate the need for the min-base-count check that currently happens prior to Trinity, so maybe we can remove that, now that a more informative error is being captured instead?

[yifei-men]

This should be addressed by https://github.com/dnanexus/viral-ngs/commit/478b823faf1d1d96df472f9eb6b7558f2e2ac52f (awaiting CI tests)

But knowing my knack for typos, is there any easy-to-reproduce dataset that we can use to trigger this error and see that it's captured accurately? I see that it's tested in your own CI tests. Does this basically involve passing an empty bam file as input?

cc @tomkinsc

[dpark01]

Passing an empty bam file as input should reproducibly create that error!

[yifei-men]

👍 awesome, thanks Danny

[yifei-men]

Manually validated in this job

The error email looks like this:

This seems a little ungrammatical... I'll change the verbiage to "detailed logs."

[yifei-men]

Addressed by #20