MultiQC Fastp and Qualimap results intergration.

sanjaynagi / AmpSeeker

A snakemake workflow for amplicon sequencing

https://sanjaynagi.github.io/AmpSeeker/

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MultiQC Fastp and Qualimap results intergration. #73

Closed ChabbyTMD closed 1 year ago

ChabbyTMD commented 1 year ago

Adds fastp and qualimap results into multiqc report. In this PR;

Updated MultiQC wrapper to 2.2.1
Explicitly declare MultiQC dependency to 1.14
Added custom MultiQC config file to override default search patterns for workflow specific filenames and patterns for fastp and qualimap metrics.
Deactivated MultiQC report generation in CI (Temporary Fix for Qualimap Issue.)

sanjaynagi commented 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.

sanjaynagi commented 1 year ago

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.

sanjaynagi commented 1 year ago

No idea what this stupid error is now, bloody qualimap java crap

sanjaynagi commented 1 year ago

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.