Test single vs paired end bam files

[olgabot]

1. Add a test configuration using this single-end bam and bai file:

• bam
• bai

2. Add a bamPaths parameter to nextflow.config like readPaths for testing

3. Update the bam file parsing as in Support input of multiple bam files with --bam '*{.bam,.bam.bai}' #19 (maybe not necessary, but would make downstream stuff easier)

4. Update the samtools_view_fastq process to (approximately):

	output:
	set val(interval_name), file("*.fastq.gz") into ch_intersected

if (params.paired_end) {
"""
samtools view -hu $bam '${chrom}:${chromStart}-${chromEnd}' \\
  | samtools fastq -N -1 ${interval_name}_R1.fastq.gz -2 ${interval_name)_R2.fastq.gz
} else {
  samtools view -hu $bam '${chrom}:${chromStart}-${chromEnd}' \\
		| samtools fastq -N - \\
		| gzip -c > ${interval_name}.fastq.gz
}

5. Make sure tests pass! :)