Constant increase in threads with comma separated list of input files and --parallel parameter

[FelixKrueger]

We have been made aware that the specifying a comma separated list of input files in conjunction with the parameter --parallel [cores] seems to lead to a continuous rise of spawned Bismark threads. This would be unintended and prone to fail at some point.

A sample command line with the 3 times the same simulated Yeast FastQ files (with different names for clarity) looks like this:

bismark --genome /bi/scratch/Genomes/Yeast/Saccharomyces_cerevisiae/SGD1/ -1 R1.fastq,simulated_1.fastq,ZZZ_R1.fastq -2 R2.fastq,simulated_2.fastq,ZZZ_R2.fastq --multicore 4

[FelixKrueger]

It turned out that for this we only had to properly exit all child processes once the mapping and merging had finished so that they do not also continue to process read pairs 2, 3 and so on...