Christopher Schröder

From my experience you can have as much threads fro the sorting as you have for bwa. If you observe the mapping behaviour, you can see it performs its operation...

I will try to do that. The mem_gb=3, is this just a rough guess? For example, I think SnpEff requires more than 3gb, but it might also depend on the...

Another question: I see the benefits for dealing only with "gb", but it would also be possible to allow other units, like 512m. What if the user wants to set...

I have a suggestion. The metric unit prefixes _T_, _G_, _M_, _k_, _h_ and _da_ are independent of the unit itself. So it would be great, if snakemake would support...

@dlaehnemann @johanneskoester @tdayris Blame shows you as author of this snippet. I can modify / fix that, but I don't see the point having this at all. bwa mem 2...

I slept on it and realised that I'm going to modify the wrapper for cram output anyway. Since samtools sort needs the reference, input.ref makes sense. I am still against...

Hey, I can implement this by first creating some snakemake wrappers for fastp and pear. Just because I'm interested: what are the benefits of fastp and pear?

What does the error message fatal: Invalid symmetric difference expression master...4367e13fcb838e5fe62ffdcb5e591461d90b334e mean?

gridss.sh is already broken into these pieces. But the execution is iteratively in bash. Now with each step beeing a rule, they can be performed in parallel. Also not every...

I would really appreciate to have this PR merged