Marcel Martin

I can now confirm that this fixes the problems with the assertions. There are still some other issues, but I can work around them by choosing the parameters slightly differently....

I’ve encountered this as well. My workaround is to use `workflow.basedir` instead of `workflow.source_path()`. Example: ```snakemake rule: output: "out.txt" params: script=Path(workflow.basedir) / "myscript.py" shell: "python3 {params.script} > {output}" ```

@aliciaevans Can I suggest to post about the bot also in the announcements issue #33333? Regarding feedback, I encountered the bot the first time in #51125 just now and at...

> I am wondering if `strobealign --create-index -r 150` and `strobealign --aemb --use-index` (no flag `-r 150`) will result in the index being regenerated(?) If the index was created with...

> (1) the two lines `Processing paired-end reads in abundance estimation mode using 32 threads` and `Total time base level alignment (ssw): 170.01 s.` > > seem incompatible since aemb...

There’s no explicit threshold. The implicit requirement is that there is at least one seed in the query that can also be found in the reference. Our seeds are randstrobes...

You get more than just one randstrobe per query. For a 150 bp read, for example, you get about 30 on average (they overlap each other). As long as one...

No, there’s no threshold either, but there is soft clipping: If extending the alignment fully towards the 5' or 3' end would lead to a bad alignment score, the alignment...

> If I use an `--aemb` flag, I don't have `sam` to filter. Do short alignments show up in the resulting `tsv`? In the `.tsv` that you get with `--aemb`,...

Thanks, let’s just merge this as it is. Other improvements can be made separately.