Currently, the pipeline has a rule which splits the bcftools merge step into two groups, as when running more than 1000 samples, bcftools merge fails. It also means the pipeline can fail if there are less than 1000 samples.
We should write this so that this is automated, I.e merging is only done in 2 steps if there are more than 1000 samples.
sanjaynagi
commented
2 years ago
Currently, the pipeline has a rule which splits the bcftools merge step into two groups, as when running more than 1000 samples, bcftools merge fails. It also means the pipeline can fail if there are less than 1000 samples.
We should write this so that this is automated, I.e merging is only done in 2 steps if there are more than 1000 samples.