Add stub directives to all processes to enable Nextflow's -stub dry-run option

[nrminor]

A user recently requested a Snakemake-like dry run feature to suss out how the pipeline works before supplying large input files. Implementing this in Nextflow is much more involved, as it requires that we write a stub directive for every single process. Fortunately, that will be relatively straightforward if tedious in this pipeline because most processes produce a single output file. Given that, a process that looks like this:

process CLUMP_READS {

    /* */

	tag "${sample_id}"

	errorStrategy { task.attempt < 3 ? 'retry' : 'ignore' }
	maxRetries 2

	cpus 4

	input:
	tuple val(sample_id), path(reads)

	output:
	tuple val(sample_id), path("${sample_id}.merged.fastq.gz")

	script:
	"""
	clumpify.sh in=${reads} out=${sample_id}.merged.fastq.gz t=${task.cpus} reorder
	"""

}

Would become this:

process CLUMP_READS {

    /* */

	tag "${sample_id}"

	errorStrategy { task.attempt < 3 ? 'retry' : 'ignore' }
	maxRetries 2

	cpus 4

	input:
	tuple val(sample_id), path(reads)

	output:
	tuple val(sample_id), path("${sample_id}.merged.fastq.gz")

	script:
	"""
	clumpify.sh in=${reads} out=${sample_id}.merged.fastq.gz t=${task.cpus} reorder
	"""
	
	stub:
	"""
	touch ${sample_id}.merged.fastq.gz
	"""

}