更新 'workflow.wdl'

workflow.wdl

@@ -12,30 +12,31 @@ import "./tasks/tmb.wdl" as tmb
 
 
 workflow {{ project_name }} {
-	#sample info
-  File? normal_deduped_bam
-  File? normal_deduped_bam_bai
-	File? tumor_deduped_bam
-	File? tumor_deduped_bam_bai
-  String sample_id
-	String Seq_platform
-	#reference fasta
+ 	#sample info
+ 	File? normal_deduped_bam
+  	File? normal_deduped_bam_bai
+  	File? tumor_deduped_bam
+  	File? tumor_deduped_bam_bai
+  	String sample_id
+  	String Seq_platform
+  	#reference fasta
 	String ref_fasta
 	File ref_fasta_dir
+  	String ref_bed
 	File annot_gff
-  File dbsnp_dir
-  File dbmills_dir
-  String dbsnp
-  String db_mills
+  	File dbsnp_dir
+  	File dbmills_dir
+  	String dbsnp
+  	String db_mills
 	File germline_resource
 	File germline_resource_tbi
 	File annovar_database
-  File? regions
-  File baseline
-  File hg38_CDS
+  	File? regions
+  	File baseline
+  	File hg38_CDS
 
 	#docker
-  String docker_fastp
+  	String docker_fastp
 	String docker_sentieon
 	String SENTIEON_LICENSE
 	String docker_qualimap
@@ -43,16 +44,16 @@ workflow {{ project_name }} {
 	String docker_strelka
 	String docker_bcftools
 	String docker_annovar
-  String docker_tmb
-  String docker_MSIsensor
+  	String docker_tmb
+  	String docker_MSIsensor
 
 	#config
-  String cluster_config
-  String disk_size
+  	String cluster_config
+  	String disk_size
 	Boolean? fastqc
 	Boolean bamqc
 	Boolean Annovar
-  Boolean AF_filter
+  	Boolean AF_filter
 
 
 if (normal_deduped_bam != ""){
@@ -97,20 +98,7 @@ if (tumor_deduped_bam != ""){
 
 	}
 
-call MSIsensor.MSIsensor as MSIsensor {
-    input:
-    sample=sample_id,
-    fasta=ref_fasta,
-    ref_dir=ref_fasta_dir,
-    normal_bam=Sentieon_BQSR_normal.recaled_bam,
-    normal_bam_index=Sentieon_BQSR_normal.recaled_bam_index,
-    tumor_bam=Sentieon_BQSR_tumor.recaled_bam,
-    tumor_bam_index=Sentieon_BQSR_tumor.recaled_bam_index,
-    baseline=baseline,
-    docker=docker_MSIsensor,
-    cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
-    disk_size=disk_size
-  }
+
 
 
 call Haplotyper.Haplotyper as Haplotyper {
@@ -215,7 +203,7 @@ call strelka_calling.strelka_calling as strelka_calling{
 		ref_fasta = ref_fasta,
 		ref_dir = ref_fasta_dir,
 		sample_id = sample_id,
-		
+		ref_bed = ref_bed,
 		docker=docker_strelka,
 		cluster_config="OnDemand bcs.ps.g.6xlarge img-ubuntu-vpc",
 		disk_size=disk_size