Dynamically change the number of cpus used in the multithreaded tools

[soulj]

The task.cpus parameter should allow passing of the nextflow config set number of cpus for a task to be passed into each command line or Rscript. Affected modules include those for kallisto, trimmomatic, sra, RNA-seq differential expression.
e.g

process INDEX {

  input:
    path transcriptome

  output:
    path 'index'

  script:
    """
    salmon index --threads $task.cpus -t $transcriptome -i index
    """
}

To view the number of cpus with squeue:

squeue -o"%.7i %.9P %.8j %.8u %.2t %.10M %.6D %C"