Wolfgang Maier

@EngyNasr @bebatut I don't see much value in offering the single-sample workflows, when collection-based flavors exist that could be run with 1-element collections. Having the single-sample WFs published would just...

@EngyNasr can you please run some json reformatter tool over your workflows. Single-line JSON is just not very nice to review and prevents meaningful diffs. Use, e.g., `python3 -m json.tool...

@EngyNasr two questions on the latest preprocessing version: - why is the host ID now not a WF parameter anymore? You could use the "Map parameter value" expression tool to...

The Pathogen-Detection-Nanopore-All-Samples-Analysis WF needs much better annotations and input dataset labels to make it understandable what it is good for. Right now, understanding the purpose without knowing the tutorial is...

The VFs accessions branch of that WF also seems to have quite some room for simplification: - Replace parts of text has a repeat element so steps 14, 17 and...

but with the smaller DB, the WF would not be production-ready? I guess an "easy" way to shrink the DB size for this case here would be to exclude human...

Hmm, not sure what the issue is with bamleftalign during linting.

I should, yes :)

@PlushZ @bebatut this looks more or less fine, but I have more of a general question: - this WF is *very* similar to https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling - regarding the differences I'm not...

@PlushZ it seems the output of samtools depth is not exactly valid input for freyja demix - see https://help.galaxyproject.org/t/freyja-module-not-working/12425. Looks like freyja expects the depth in the fourth column instead...