Describe how to view multiple multiQC outputs #4779
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| > - {% icon param-repeat %} *"Insert FastQC output"* | ||
| > - *"Type of FastQC output?"*: `Raw data` | ||
| > - {% icon param-files %} *"FastQC output"*: 4 `Raw data` outputs of **FastQC** {% icon tool %} | ||
| > 4. {% tool [MultiQC](toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0) %} with the following parameters: |
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Why do you not use fastp for fastp output?
Such a change should probably also be reflected in the workflow coming with the workflow, or?
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yeah totally, we have the Fastp step in the workflow included in the training material, which shows everything, including the number of reads before and after trimming, which trainers has to check to answer the training question
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You mean fastp as input to mutliQC or looking at the output of fastp ?
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Fastp output will only show you the difference before fastp and after fastp; but there is also a porechop step in between. So fastqc will give you the difference between raw reads and all QC steps.
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Then you should should include also the other fastqc output. Currently the tutorial runs fastqc twice. Once before porechop and fastp and once after. Just add the additional FastQC report, or?
Probably you can do this in the same MultiQC run (maybe name the different FastQC reports .. such that you can distinguish before and after)
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In order to show multiple fastqc reports in multiQC one needs to rename the input elements for fastQC, since this part:
>>Basic Statistics pass
#Measure Value
Filename Barcode11_Spike2b_fastq_gz.gz <<<<<<<<<<<<<<<<
File type Conventional base calls
Encoding Sanger / Illumina 1.9
is leading to the not rendering of the duplicated file names.
And that would mean to use Extract element identifiers, regex, Relable for each additional multiQC input, that looks rather complicated and difficult for the students to follow. And also takes me to long to fix for tomorrow.
But I think @EngyNasr will fix it for IWC and then we can update here as well.
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Since we anyway to late for the training today, I will collect some more changes here and fix it the right way after all. |
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Next one: |
We need a quick fix, since we run a training tomorrow.
The issue is that multiQC does only show one file / collection; if the file names are the same.
Now we run multiQC twice.