Arya Massarat

just chiming in to say that I'm encountering this issue, as well thanks for creating a fix for this!

I think this PR can be closed, since #288 has been merged, and I believe it already implements this fix?

What shell are you using? When you run `echo $0` outside of Snakemake, does it say `/usr/bin/bash`? Is `conda` available in the bash shell `/usr/bin/bash` as well as whatever shell...

hmm, I'm not sure then... You could maybe try this: 1. Run and enter the bash shell at `\usr\bin\bash`: ``` \usr\bin\bash ``` 2. Check if `conda` is in your `$PATH`:...

Hi @snajder-r , You can [refer to `output` in `params` using a lambda function](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules). Here's a common refrain that I like to use in these situations. ``` params: outdir =...

Yeah, it would be nice if it went both ways. I'm no Snakemake expert, but I think the way that rule dependencies are resolved requires that the output be a...

> This made me think of another possible workaround Yup, I think that should work, too!

Hopefully someone can figure out how to resolve the circularity issue and make `params` available in `output` @tgelafr1, in the meantime, you might be able to achieve the desired behavior...

Hi @Rubbert, Yes, VarCA was built and tested with paired-end reads, but in theory, it should be possible to coerce it into using single-end reads if you skip the peak...

@patrick91, great thanks! I'll try it out can you say a bit more about why this works?