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- Always use spaces (not tabs!) in the multiqc_config.yaml file.
- Make sure the file is saved with Unix line endings (not Windows or Mac).
- Pay attention to the output when running multiqc. It will tell you if there are issues parsing the config file.
- Always delete any previous MultiQC output files before running multiqc
- While their documentation says existing files will just be updated, I have seen MultiQC get confused when previous reports exist.
- It is a good idea to change the name of the MultiQC output files
- If output files with those names are not created, something went wrong!
- Consult example config files
- An example multiqc_config.yaml file: https://github.com/ewels/MultiQC/blob/master/multiqc_config_example.yaml
- All multiqc_config.yaml defaults: https://github.com/ewels/MultiQC/blob/master/multiqc/utils/config_defaults.yaml
- Avoid running multiqc on large complex directory trees.
- Instead, create a separate directory (or directory tree) only for MultiQC
- Copy or link the files you want MultiQC to look for there, and use it as MultiQC's target directory.
- MultiQC will run much faster and have fewer confusions.
- Instead, create a separate directory (or directory tree) only for MultiQC
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