The latest version of MultiQC doesn’t seem to support Custom content when using MultiQC in a workflow. I combine multiple different results into MultiQC using the custom content feature and it worked well with the old version. When i changed it to the new version it no longer works. I have gone back to the old version, however i like the export as CSV function of the new Version. Is this just a bug since this latest version is still quite new? Happy to share workflows/ histories
Hi @jessemartin
Yes, sharing your examples would be great to help clarify. 
And as an example from us, this was a recent topic where a public workflow was adjusted to use a custom input for a tool option. I’m not sure which option/tool versions you have exactly yet, but maybe helps to frame what is possible? VGP- unable to select or add hind3 restriction enzyme to Hi-C scaffolding workflow - #2 by jennaj
Let’s start there!
Hi Jenna,
I was using the MultiQC 1.11+galaxy1 version and the Custom content feature which allows tables to be reported was working fine in my workflow, but the newer version no longer seems to work. If i try each table individually with the new version it works fine, however it wont work in my workflow.
Below are 2 histories where the only difference is in the version of MultiQC used for reporting
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Hi @jessemartin
First, thank you SO MUCH for sharing your data. I don’t think I would have figured this out without all those details.
So … it seems that the updated tool version is having trouble parsing certain line formats into a table. Specifically, comment lines that start with a hash #. The prior version seems to have been stripping the hash and space out, or just ignoring it, when populating the final table. The only file you had like this is the quast “tabular report”.
If I remove those leading hashes in that single input file, with no other changes, everything works fine. I’ve done that in my copy of your history below. Notice that I used a tool that you can also add to your workflow (sed) with a simple substitution command.
Now, why the new MultiQC tool version is different, and if we can do something about that with the Galaxy MultiQC wrapper itself, I’m not sure yet… I’ll be exploring it next, and will come back here with an update. But I wanted to get you a solution now, so you don’t need to wait.
Update: Ticket below for tracking. What was observed might be QC trapping of non-standard tabular data internal to the tool but the developers can help to sort out what the details are, and how to handle it.
- Request: Make MultiQC 1.24.1+galaxy0 custom parsing backwards compatible with 1.11+galaxy1 · Issue #6335 · galaxyproject/tools-iuc · GitHub
- Note: In the prior version, the table output was ignoring any lines that started with a hash # character, and not printing them out to the MultiQC summary. To exactly replicate: you could pre-filter out the # lines, instead of exposing them as I did in my tests. The point is to not send # lines to the tool for this function to avoid the QC check failing the tool.
Wow, not so easy to solve but so glad to see you are really making use of workflows and advanced functions!! Please give this a review and let us know if this also works for you. One additional manipulation shouldn’t be too difficult to add into your workflow and test, and we can follow up if I missed something.
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