Multiple subsampling from same alignment


with the ncov workflow, is it possible to make multiple subsampling build without realigning data (ncov/results/aligned_MyBuild.fasta) for each build. I guess we need to edit the Snakefile but I’m not sure where exactly.


Hi Eric - each input is only aligned once, and then multiple builds can use that alignment (Snakemake code is here).

Each build can define a different subsampling scheme (or the same scheme with different wildcards) - here’s an example of such a workflow config.

P.S. input is each entry in the builds.yaml→inputs whereas a build is defined in builds.yaml→builds and each build uses the combined data from all inputs + a subsampling scheme.

Thank you James. This is exactly what I needed