Lucas Czech

Hey MK, thanks for using grenedalf! 1. You can indeed filter input via `--filter-region-gff`, but as you say, this will _keep_ the sites in the GTF, not remove them. Unfortunately,...

Of course, if all you need from the GFT is the regions to remove, you can also convert this into one of the other file formats, and use those as...

Hi Joanna, thanks for your interest in grenedalf! Unfortunately, at the moment, the CMH test is not implemented in grenedalf. It has been on my list for a while though,...

Hi Joanna, thanks for the update and the inspiration for the LRT, I'll have a look at that. As for your commands to remove the sync extensions that PoPoolation2 does...

It gets a bit weirder: The output of `print` in my production pipeline is not printed to terminal on the first "fresh" run of snakemake (on an empty `--directory`). It...

One more observation: In my production workflow, it seems that the DAG re-evaluation triggered by checkpoints also has an interesting effect on the logging: the subprocess used for the re-eval...

Hi @cademirch, thanks for the quick reply! > I'm not sure what to think about the printing issue, I don't fully understand it as you've described here so perhaps an...

Feel free to [copy what you need](https://github.com/moiexpositoalonsolab/grenepipe/blob/53912b0749f90c7c29ecde2855657318e1269020/workflow/rules/initialize.smk#L77-L214)!

Quick follow-up question in the meantime: For my extra log file, I used to be able to distinguish between the main process and the child processes, in order to put...

Agreed, this is making my GitHub wiki hard to read at times. Using `nowrap` would greatly improve this! I tried messing around with `` myself, but that is all ignored/sanitized...