mapping task zcat

tasks/mapping.wdl

@@ -15,13 +15,13 @@ task mapping {
 		set -o pipefail
 		set -e	
 
-		STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --runThreadN 20 --outFileNamePrefix OnePass_ 
+		STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix OnePass_ 
 
 		genomeDir=./twoPass
 		STAR --runMode genomeGenerate --genomeDir $genomeDir --genomeFastaFiles ${STref_dir}/${fasta} --sjdbFileChrStartEnd OnePass_SJ.out.tab --sjdbOverhang 75 --runThreadN 20
 
 
-		STAR --genomeDir $genomeDir --readFilesIn ${fastq_1} ${fastq_2} --runThreadN 20 --outFileNamePrefix ${sample}_
+		STAR --genomeDir $genomeDir --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_
 	>>>
 
 	runtime {