nextflow.preview.dsl=2
params.genome = ''

process BOWTIE2 {
	// depending on the genome used one might want/need to adjust the memory settings.
	// For the E. coli test data this is probably not required

	// label 'bigMem' 
	// label 'multiCore'
		
    input:
	    tuple val(name), path(reads)
		val (outdir)
		val (bowtie2_args)
		val (verbose)

	output:
	    path "*bam",  emit: bam
		path "*stats.txt", emit: stats 

	publishDir "$outdir/bowtie2",
		mode: "copy", overwrite: true

	script:
		if (verbose){
			println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
		}

		cores = 4

		readString = ""

		// Options we add are
		bowtie2_options = bowtie2_args
		bowtie2_options +=  " --no-unal "  // We don't need unaligned reads in the BAM file
		
		// single-end / paired-end distinction. Might also be handled via params.single_end 
		if (reads instanceof List) {
			readString = "-1 " + reads[0] + " -2 " + reads[1]
		}
		else {
			readString = "-U " + reads
		}
		
		index = params.genome["bowtie2"]
		bowtie2_name = name + "_" + params.genome["name"]

		println ("bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString}  2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam")
		"""
		bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString}  2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
		"""

}