straingr compare all vs all deon't create output file.

[SilasK]

I asume that one cann supply more than 2 hdf files to straingr compare --all-vs-all even it's not clear from the docs.

However no output file are created. Neither the pairswise summary files, nor a combined summary file.
The log contains the subcomands for all pairs, no error message.

How should I use this command?

[lrvdijk]

I'll have to document this command a bit more indeed. The idea is that straingr compare --all-vs-all outputs a shell script with per line a new straingr compare command line invocation, but for an individual pair of samples.

So, if you execute the output with bash, after it finishes all comparisons should be ready.

The idea behind this file is that instead of executing it sequentially with bash, you also easily execute all comparisons in parallel on a HPC, where each cluster job executes one line. Hope it makes it a bit more clear.