Fix number of CPUs in piped commands

[jfy133]

Basically this: nf-core/modules#499

[jfy133]

Processes to update:

• AdapterRemoval
• bwa aln
• bwa mem
• bam filtering
• bedtools
• pmdtools(? mc_small but no specification of CPUs?)
• pileupcaller (? mc_small but no specification of CPUs?)

[jfy133]

Most of these the multiprocessing is with pigz, so probs can just ${task.cpus - 1}