Add FASTQ files to testing operations

[adamrtalbot]

This PR adds the ability to use the FASTQ files in downstream operations (e.g. rename, compress). This will allow us to add larger input files into the mix for pushing the limits of testing a bit more based on requirements.

[drpatelh]

Suggested change

	params.total_reads = 10000 // Total number of reads per file (10k reads generates a ~1GB file)
	params.num_files = 10 // Number of FASTQ files to generate in parallel and concatenate
	params.small_files = 1000 // Number of small files to generate in a single process
	params.run = null // Tools to selectively run
	params.skip = '' // Tools to selectively skip
	params.use_small_files = true // Use small files in downstream operations
	params.use_fastq_files = false // Use FASTQ files in downstream operations
	params.large_file_types = 'fastq' // Number of FASTQ files to generate in parallel and concatenate
	params.small_file_types = 'fastq,dev0' // Number of FASTQ files to generate in parallel and concatenate
	params.large_num_files = 10 // Number of FASTQ files to generate in parallel and concatenate
	params.small_num_files = 1000 // Number of small files to generate in a single process
	params.fastq_total_reads = 10000 // Total number of reads per file (10k reads generates a ~1GB file)
	params.run_processes = null // Tools to selectively run
	params.skip_processes = '' // Tools to selectively skip
	//params.use_small_files = true // Use small files in downstream operations
	//params.use_fastq_files = false // Use FASTQ files in downstream operations

[adamrtalbot]

Note: this is a much lighter weight version of #5 which may be a better long term solution. This one is backwards compatible while PR #5 is not.