rna-seq-tophat/tasks/trimmomatic.wdl

task trimmomatic {
	File read1
	File read2
	File adapter
	String base = sub(basename(read),"\\.\\S+$", "")
	String docker

	command {
  	trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  -baseout ${base}.fq.gz ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
	}

	runtime {
		dockerTag: docker
	}

	output {
		File read_1p = base + "_1P.fq.gz"
		File read_2p = base + "_2P.fq.gz"
	}
}