input revised

tasks/samtools.wdl

@@ -4,7 +4,6 @@ task samtools {
     String bam = base + ".bam"
     String sorted_bam = base + ".sorted.bam"
     String sorted_bam_index = base + ".sorted.bam.bai"
-    String viral_samstats = base + ".viral.samstats"
     String docker
     String cluster
 
@@ -14,7 +13,6 @@ task samtools {
        /opt/conda/bin/samtools view -bS ${sam} > ${bam}
        /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
        /opt/conda/bin/samtools index ${sorted_bam}
-       /opt/conda/bin/samtools stats ${sorted_bam} > ${viral_samstats}
     >>>
 
     runtime {
@@ -27,7 +25,6 @@ task samtools {
     output {
       File out_bam = sorted_bam
       File out_bam_index = sorted_bam_index
-      File out_viral_samstats = viral_samstats
     }
 
 }

workflow.wdl

@@ -6,9 +6,8 @@ workflow {{ project_name }} {
 
 	File read1
 	File read2
-        File idx
+    File idx
 	String idx_prefix
-        File gtf
 	
 	
 	call hisat2.hisat2 as hisat2 {