An interactive web tool reported in the BC2 conference in Basel- BigMAG:https://github.com/jeffe107/BIgMAG

Ooooh

Hi, James. Yes, actually at the beginning we were thinking of BIgMAG as a plugin for nf-core/mag; however, the main goal was to benchmark pipelines, and therefore it would not be fair for the other pipelines that do not have the same tools as nf-core/mag. Anyway, I think that now "it should not take too much work" to adjust BIgMAG to receive the output from nf-core/mag.

Makes a lot of sense, and I agree with more freedom to the user! Should I make an issue on the BIgMAG repo? or talk about it somewhere else?

Actually, I think the other way around: what we have to adjust is the output from nf-core/mag, I mean we could create a specific channel from each of the tools that BIgMAG displays to collect the data and have the single file at the end of nf-core/mag execution

Ah got you!

That is a long story thath I will try to make short: the dashboard is based on Dash, and Dash is not thought to be self-contained (they are aiming to sell hosting the apps). That's why we have this lite version of BIgMAG, but it is not as interactive as the full version, and to store it as an HTML, the user has to run the app anyway

OK cool 🙂 So I guess we could have a subworkflow that gathers all the relevant metric fiels, makes

collectFile

to make the mega TSV, then an nf-core/module for BIgMAG(_lite) to generate the HTML? or?

I will check in which state nf-core/mag is now, it's been a while since the last time I run it. Afterwards, I will propose the strategy to collect the files and create the TSV file for BIgMAG

That would be great!

In short again, no, with the current state of BIgMAG, it is not possible to provide the HTML app as a result of the pipeline execution. At this moment, the users would have to run BIgMAG independently either the full or the lite version with the TSV provided by nf-core/mag

Ah sorry, I did misread your docs on that sorry! But OK, then at least preparing the file would be sufficient. Then I await your proposal! Looking forward to it!

Great, yes. We realized about this "issue" when we were about to finish, because what we wanted was something like MultiQC reporting 😢

Happens to the best of us 🙃

hahahah. BTW: thank you for the great job with nf-core/mag. It was a Bible for me during two years

haha, well I would thank people like @hadrien @Sabrina Krakau and @Daniel Straub, as they are the architects! I'm just keeping it going!

Hi @James Fellows Yates I just wanted to let you know that I already created a PR (#860) to include the subworkflow to generate the file for BIgMAG.

Whooop! Thank you! I normally work on Fridays on mag, so I will probably get to it then 🙂, but I'll do a quick look now