Alter: input

inputs

@@ -1,6 +1,6 @@
 {
   "{{ project_name }}.panel_id": "{{ panel_id }}",
-  "{{ project_name }}.sample_bam_bai": {{ sample_bam_bai | tojson }},
+  "{{ project_name }}.normal_recaled_bam_bai": {{ normal_recaled_bam_bai | tojson }},
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
   "{{ project_name }}.dbsnp": "{{ dbsnp }}",

tasks/PON.wdl

@@ -2,8 +2,6 @@ task PoN {
 
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
-	String sample
-
 	File ref_dir
 	String fasta
 	File cosmic_dir
@@ -14,6 +12,7 @@ task PoN {
 
 	File normal_bam
 	File normal_bam_index
+	String sample=basename(normal_bam, ".*")
 	String docker
 	String cluster_config
 	String disk_size

workflow.wdl

@@ -27,9 +27,8 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		ref_dir=ref_dir,
 		regions=regions,
-		sample=item[0],
-		normal_bam=item[1],
-		normal_bam_index=item[2],
+		normal_bam=item[0],
+		normal_bam_index=item[1],
 		cosmic_vcf=cosmic_vcf,
 		cosmic_dir=cosmic_dir,
 		dbsnp=dbsnp,