rna-seq/tasks/trimmomatic.wdl

task trimmomatic {
	File read1
	File read2
	File adapter
	String baseout
        String baseout_gz = baseout + ".fq.gz"
	String docker
	String cluster

	command {
           /opt/conda/bin/trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  -baseout ${baseout_gz} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
        }

        runtime {
	   docker: docker
	   cluster: cluster
	}

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