Add threads to BWA/Samtools commands

The nextflow config increases the number of CPU with each task

prod.config

withLabel: samtools {
		module = ['bioinfo/samtools-1.14']
		cpus = { 6 * task.attempt }
	    memory = { 8.GB * task.attempt }
	    time = { 3.h * task.attempt }
	}
	
	withName: BWA_ALIGNMENT {
		cpus = { 6 * task.attempt }
	    memory = { 8.GB * task.attempt }
	    time = { 3.d * task.attempt }
	}

But the commands do no include a thread number, so only one CPU is used.

bwa mem ${reference} ${reads} 1> ${sample}_${referenceName}.sam 2> ${sample}_${referenceName}.log
samtools view -bS ${sam} > ${sample}.bam

For bwa mem it's the -t argument, and for samtools sort it's -@. Not sure it's possible for the other samtools tools, so no need to increase threads in the nextflow config to avoid waiting in pending for nothing.