se_hisat_0605

tasks/samtools.wdl

@@ -18,7 +18,7 @@ task samtools {
        /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
        /opt/conda/bin/samtools index ${sorted_bam}
        /opt/conda/bin/samtools view -bs 42.1 ${sorted_bam} > ${percent_bam}
-       /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${sample_id}.ins_size
+       #/opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${sample_id}.ins_size
     >>>
 
     runtime {
@@ -32,7 +32,7 @@ task samtools {
       File out_bam = sorted_bam
       File out_percent = percent_bam
       File out_bam_index = sorted_bam_index
-      File out_ins_size = ins_size
+      #File out_ins_size = ins_size
     }
 
 }

workflow.wdl

@@ -182,4 +182,4 @@ workflow {{ project_name }} {
                 gene_abundance = stringtie.gene_abundance,
 		count_length = count_length
 	} 
-}
+}