MultiQC in RNA-seq Primary Analysis workflow


I am the admin for the Galaxy instance that we use at our institution, which is connected to a High-performance cluster as well. I have developed an RNA-Seq Primary analysis workflow and have incorporated the “MultiQC” tool. In this workflow, I have fastQC, cutadapt, STAR, featureCounts in my workflow, and multiQC has been put in for each tool so the output of each is provided so that a multiQC report is generated for each. I would like to use MultiQC so that it generates one multiQC report for all the tools rather than 4-5 different reports. The multiQC tool in Galaxy didn’t have such an option available. Is there a way to create one single multiQC report for all tools in the workflow? Any help or suggestions are appreciated.

Thank you,

Hi @Priyanka_Bhandary

Each tool reports different information for the summary that MultiQC creates. Meaning, it works that way in Galaxy or otherwise.

Including new “Insert Results” sections is how to list those different statistics from different tools together. Did you see that option or am I misunderstanding what you want to do?

Technically, you could create a custom report of just the information you want to capture. Example: maybe you want to summarize how many reads survived each step. That would involve custom data manipulations to capture a statistic for each data input/output/tool, and all results would need to have the same formatting before inputting them to MultiQC for the summary generation. The option to use a custom report is the last item in the Which tool was used generate logs? pull down menu, and will take some exploration on your part to get it to work. But, certainly seems possible.