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echo '<password>' | docker run --rm -i ruphin/htpasswd '<username>'

Keep in mind that running this in your consile directly means everything is stored in your bash history. It should be safe when run from bash scripts and the like.

Writing the output to file

It's all bash, so you can write the output directly to a file:

echo '<password>' | docker run --rm -i ruphin/htpasswd '<username>' > .htpasswd
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