I recently changed --consMemory to override the memory specification for hal2vg as well as halAppendCactusSubtree, in addition to cactus_consolidated.
But it seems that in doing so, I broke the automatic estimation when --consMemory isn't used. The net effect is that these jobs would get the default-memory (2G) no matter what if nothing was specified with --consMemory.
This PR should correct this by adding a separate memory override option to these functions. The initial bug was because toil's memory option was being used before, but I was checking it after it was getting filled in with its default value.
I recently changed
--consMemoryto override the memory specification forhal2vgas well ashalAppendCactusSubtree, in addition tocactus_consolidated.But it seems that in doing so, I broke the automatic estimation when
--consMemoryisn't used. The net effect is that these jobs would get the default-memory (2G) no matter what if nothing was specified with--consMemory.This PR should correct this by adding a separate memory override option to these functions. The initial bug was because toil's
memoryoption was being used before, but I was checking it after it was getting filled in with its default value.