revise inputs

workflow.wdl

@@ -15,8 +15,8 @@ workflow {{ project_name }} {
 	File idx
 	File screen_ref_dir
 	File fastq_screen_conf
-	String idx_prefix
 	File gtf
+
 	String disk_size
 	String fastqc_docker
 	String fastqc_cluster
@@ -34,7 +34,6 @@ workflow {{ project_name }} {
 	String stringtie_cluster
 	String samtools_docker
 	String samtools_cluster
-	Int insert_size
 	String qualimap_docker
 	String qualimap_cluster
 	String ballgown_docker
@@ -57,6 +56,7 @@ workflow {{ project_name }} {
 	Int qualified_quality_phred
 	Int length_required1
 	Int disable_quality_filtering
+    Int insert_size
 
 	Boolean pre_alignment_qc
 	Boolean qualimap_qc
@@ -124,7 +124,9 @@ workflow {{ project_name }} {
 		cluster=hisat2_cluster,
 		disk_size=disk_size
 	}
-	} else {
+	}
+
+	if (!fastp_run){
 		call hisat2.hisat2 as hisat2 {
 		input: 
 		docker=hisat2_docker,