They are run in a follow-on chain and Toil apparently handles them with recursive calls. So having more than 999 results in a Python exception about a recursion limit being exceeded.
The default batch size is 50. This PR will boost it to whatever's needed (with a warning) to keep the number of jobs comfortably under 999, allowing inputs of more than 50k genomes to run through (this part of the pipeline) ok.
They are run in a follow-on chain and Toil apparently handles them with recursive calls. So having more than 999 results in a Python exception about a recursion limit being exceeded.
The default batch size is 50. This PR will boost it to whatever's needed (with a warning) to keep the number of jobs comfortably under 999, allowing inputs of more than 50k genomes to run through (this part of the pipeline) ok.