Hello,
I was wondering if anyone does unit-testing for NGS pipeline that follows GATK best practice and is written in bash ?
From what I understand- unit testing is done by developers who writes their own code that include functions.
Can it be done for a fairly basic piece of code that stitches various software together (bwa-picard-GATK) ? An example or links would be useful.
Many thanks
Thank you. So its for GATK 3.7. So if I understand your statement correctly, the verification would just be testing if the paths to the input/output folder is correct, the software generates the expected output for the next step etc. This would be mainly (not limited to) include if-else, echo statements in bash? Again, Travis CI/Jenkins/Circle CI - these are for developers, I assume or can they be used for something as basic as alignment (bwa) to mark dup (picard) to variant calling (gatk 3.7)?
No, the Pipeline I put up as an example up there with a link to Github checks more than just paths: The tests that run there with TravisCI run a typical pipeline with some example data and check whether this runs/works well.
You can basically run any kind of testing script with these services - but would need docker or something to ship your tools in an efficient way to the testservers.