Write custom test for checking contents of BAM file. about modules HOT 3 CLOSED

I think we can get away by importing the SAMTOOLS_FLAGSTAT in every module that generates a BAM file and checking the md5sum of that. If the SAMTOOLS_FLAGSTAT process fails then it will almost certainly indicate that the BAM file is corrupted.

The only downside is that we will need to pull another container for the test but I don't see a way around that even with custom tests. We will need something that can read BAM files 🤷🏽

from modules.

I was thinking we essentially run the same thing SAMTOOLS_FLAGSTAT is doing but in pytest-workflow, possibly even with pysam but I don't want to add another outside dependancy for testing. Plus I think the nextflow will be easier for everyone to wrangle, rather than making understanding the tests a barrier for entry.

from modules.

Not sure what we can do here without adding other dependencies / chains of modules to the tests which in itself isn't ideal given that the size of the repo and tests will only grow. I suggest we leave things as they are for now and see if we can come up with a cleverer solution in the future.

from modules.