hello, I got a problem with multiQC report of FastQC output, I got a fastQC reports from a pair end collection, when I select multiQC for all my collection, then just does for 2 samples, not for the 10 samples (20 fastQC raw data for pair end colection), I already change the name for my collection to unique, and did not work, so what can I do?
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Welcome @diego_ruiz
It sounds like you are trying to address the overlapping sample name issue. We can help to sort out the final details.
For this part
Do you mean that you adjusted the collection identifiers to be distinct? This is what MultiQC will be using for the “sample” identifier.
We have an example here
In the workflow, notice how the initial paired collection is sent to the trimming tool, then the original read collection is split off and “flattened”, and the post-trimming reads are also split off and flattened and given a slightly different collection identifiers.
The modification applied to the identifiers is “MultiQC friendly” in the example. Why? MultiQC has some internal logic to sort and group samples. It is interpreting parts of the sample identifier names. This can lead to issues similar to conflicting base sample names e.g. “missing” reports.
So .. my best guess about what is going wrong with your use case is that the renamed identifiers are being interpreted in an unintended way.
You are welcome to import the workflow above and modify it for your trimming tool. Or, maybe just review what is happening, compare to your processing, and make adjustments to your workflow? If you get stuck, you are welcome to share back the workflow invocation (grants access to the workflow + history example) and we can help review to solve this. Or, you can share the history directly with the inputs/outputs from manual tool runs.
Either is fine and sometimes screenshots of that same information is enough. Hope this helps to get you started and let us know how this turns out if you resolve it on your own! 
How to share a workflow invocation
- Go to Activity bar → Workflow Invocations and click on the invocation in the listing
- Click on the Sharing icon
- Confirm in the pop-up
- The link will be copied to your clipboard
- You can paste that back here (or, in any message to a collaborator)
- When done, unshare your history → FAQ: Sharing your History
