On Mon, Apr 06, 2020 at 09:46:44PM +0200, Andreas Tille wrote: > Hi Tony, > > On Mon, Apr 06, 2020 at 12:19:17PM -0700, tony mancill wrote: > > > > I spent a while looking into this bug (and thereby took a crash course > > in the Sequence Alignment Map file format) > > May be I need such a crash course as well. ;-) > > > So I think the tool is doing the right thing outputting FAIL for these > > files. I propose that we update the test to ensure that a summary file is > > produced and contains the requisite number of lines for each of the data > > quality tests, and that each line contains one of "PASS|WARN|FAIL" to > > indicate that FastQC was able to run the tests. > > ... > > This sounds all pretty convincing. Feel free to do a team upload > implementing your suggestion.
I went ahead and implemented this as a comparison of the summary output with the "known good" output and pushed as a merge-request to Salsa [1]. I haven't done much with autopkgtests yet and hoped that someone could take a look at the change I made to exit non-zero if the comparisons fail. This seems like what we want to happen, but I wasn't sure. I tested by running autopkgtest with a good build and a "bad" build (by altering one of the expected summary output files) and I think it works as expected. If it looks okay, I can take care of the team upload. Cheers, tony [1] https://salsa.debian.org/med-team/fastqc/-/merge_requests/1
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