Closed ChabbyTMD closed 1 year ago
Hey Trevor, I've just tried to add qualimap as a shell command rather than a wrapper.
Had to make a new conda env just for it, nothing else would work. Seems to be working. Let's see how CI goes.
MultiQC is pretty awesome tbf when there are a lot of things in it!
Its even cooler that you can enter it straight through the results-book.
No idea what this stupid error is now, bloody qualimap java crap
Doesnt seem to be much re that qualimap error online.
Qualimap is working fine on my machine using that conda env, so I'm removing it from CI, the error seems to be something specific to the github actions CI system.
Also I've made the multiQC inputs depend on the config, so we can have multiqc=True, but the others False if we wanted for some reason.
Adds fastp and qualimap results into multiqc report. In this PR;