MultiQC is not recognising two folders argument

[tluquez]

Description of bug:
MultiQC, when two or more folders supplied, is not recognising the .json from fastp

MultiQC Error log:

cat .command.log
[INFO   ]         multiqc : This is MultiQC v1.6.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '.'
[INFO   ]         multiqc : Only using modules fastqc, fastp
Searching 9 files..
[INFO   ]          fastqc : Found 2 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

File that triggers the error:
MultiQC is being used as a step in a Nextflow pipelines that generates two folders with the respective output files from fastp and fastQC (nextflow_output.tar.gz) to be supplied to multiQC.

MultiQC run details (please complete the following):

• Command used to run MultiQC: multiqc fastp/ fastQC/
• MultiQC Version: MultiQC vv1.6.dev0
• Operating System: GNU/Linux 4.15.0-24-generic x86_64
• Python Version: Python 3.6.5
• Method of MultiQC installation: pip3

Additional context
When I mix both the fastQC .zip and the fastp .josn reports in the same folder I get what I want: A multiQC report with both reports (see multiqc_report_same_folder.html.zip). However, if I specified two directories to search reports in multiqc fastp/ fastQC/ it seems to recognise only the fastQC reports, thus getting a multiQC report like multiqc_report_different_folder.html.zip.

The nextflow pipeline is fastq_test.nf.zip.

[ewels]

Hi @TainVelasco-Luquez,

MultiQC finds fastp files by specifically looking for a filename fastp.json. Your nextflow results files however are called SRR5442949_fastp.json. As a result, MultiQC ignores it and only processes the FastQC results.

My suspicion is that you were adjusting the output filenames at the same time as the directory structure? I can't test my hypothesis unfortunately as the results files you sent are symlinks and not the actual output from FastQC / fastp.

You _should_ find that if you keep the default fastp filename of just fastp.json then it should work again. However, it would make sense for me to change the pattern to match *fastp.json, so I'll do that now as well...

Let me know if you make any progress!

Phil

[ewels]

Ok, I pushed the change, so if you pull the latest version of MultiQC it should now work. I'll close this issue now, but please let me know if you're still having problems.

Cheers,

Phil

[tluquez]

Hello @ewels !

Thank you again for the quick feedback.

Your suspicion was right. In the beginning I was using the raw fastp.jsonfiles, however nextflow complained about conflicting file names, when using more than two different files. So I was forced to add the sample name_fastp.jsonhoping MultiQC were able to recognise the fastp.json(that now it does :exclamation: :raised_hands:).

After updating MultiQC I got exactly what I was looking for => multiqc_report.html.zip.

Thank you very much for your help.

Cheers,

Tain

[ewels]

Great! Thanks for letting me know 👍