Requested output format changes

[andrewdavidsmith]

Hey Guilherme.

Thanks for the quick reply! Great that you've gotten the problem fixed. However, I was hoping to run falco as part of general pipeline, and we are relying on conda for managing the environment and I'd like to keep the custom parts down to a bare minimum.

Could I ask why you don't include a more stable output form, perhaps as a supplement to the fastqc like output, and write a specific falco module for multiQC? (https://multiqc.info/docs/#custom-content).

Maybe this could be a more stable way to integrate into multiQC, and also have falco being q part of the list of modules available in multiQC (raising awareness).
As we are developing pipelines for running in cloud based pipelines, core-minutes become important, and having a fast tool (like falco) is really high up on the priority list.

Originally posted by @pbiology in #7 (comment)

[nick-youngblut]

@andrewdavidsmith does falco output work directly with multiQC? It appears to based on the use of falco + multiQC in the nf-core/demultiplex pipeline, but just providing the path to the falco output summary/data files to multiQC does nothing (no output from multiQC).

A bit of docs in the README on how to integrate falco with multiQC would be great.

If falco cannot be directly integrated with multiQC, then it would be helpful to have such a warning in the README, given that developers would like to balance the trade-off of switching to falco from fastqc versus losing (simple) multiQC integration.

[andrewdavidsmith]

@nick-youngblut I can't answer your question right now. I've heard of people using it seemingly smoothly with multiQC, but I never personally have done it, so I can't say how easy it was, or what kind of issues were present. I'll try to look into it.

Most likely I'll try to add a comment in the README about this fact -- i.e., my own continued lack of knowledge on this issue, and phrased as a warning. Obviously I'm happy to receive any input you can provide if you do push forward with this.

[nick-youngblut]

I was able to get multiQC working as described by @sklages in #13. A simple description of this in the README could help users get MutliQC up-and-running with falco, without the need for trial-and-error or searching through the issues for #13

[adRn-s]

This should be considered a bug, given that it's claimed to be a drop-in replacement to fastqc. The first thing anyone would like to see are command arguments, and the second one, would be using the output with downstream tools seamlessly. MultiQC is far too popular to be ignored...

PS. Thanks for your amazing work!

[andrewdavidsmith]

@adRn-s I am labeling this as a bug, according to your suggestion -- I'm very happy to consider a PR.