Why are Fasta index and BAM index not created by distinct rules, but in the variant_calling rule?
The following seems to be suboptimal to me: https://git-r3lab.uni.lu/IMP/IMP/blob/master/rules/Analysis/variant.rule#L11 https://git-r3lab.uni.lu/IMP/IMP/blob/master/rules/Analysis/variant.rule#L18
Shouldn't the respective files be part of the input: and have a respective rule, rather than being created within the variant_calling rule, if they do not originally exist?
{input[1]}.bai is probably less of an issue as it is independent for metaG and metaT, but since {input[0]}.fai is the merged assembly of both types (mg and mt), it needs to be created only once.
Could it be that executing this rule for mg and mt in parallel could create issues/overwritings/collisions here?
Best,
Cedric