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  • Show the relevant parts of your code. Are you allowing the nextflow process that runs your python script to use 12 threads? Commented Jun 4, 2024 at 7:47
  • As suggested, please add the code for the process, workflow declaration, and config file. If you've set maxForks to less than the number of bams, then you will increase runtime. Also, with the 30 minute example, how does this bam file compare to the rest? You could have just picked a small and relatively invariant file. Commented Jun 4, 2024 at 8:57
  • @Pallie I've added the relevant code that was requested! Hopefully this helps. Commented Jun 4, 2024 at 20:58
  • @dthorbur sorry forgot to @ both of you. Commented Jun 4, 2024 at 20:59
  • Additionally, I wanted to say that I only set maxForks to see if setting a lower number of NF processes would fix the issue. It does not. For the 30 minute sample, I actually chose the largest BAM file I had to do the tests on so this BAM file IS abnormal, but it is larger than all the other ones that are being asked to be processed. Commented Jun 4, 2024 at 21:38