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Update usage.md
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jonas-fuchs authored Jun 17, 2024
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Expand Up @@ -110,10 +110,17 @@ Let's assume you have

Then with

Linux:
```shell
VARVAMP_CONFIG=custom_config.py varvamp qpcr input_alignment.fasta my_results
```

Windows:
```shell
set "VARVAMP_CONFIG=custom_config.py"
varvamp qpcr input_alignment.fasta my_results
```

you run the command with the parameter change applied.

If, as another example, you have several custom config files, each optimized for a specific use case, stored in a folder `/home/me/my varvamp configs`, you might want to run:
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