vcf name

README.md

@@ -2,7 +2,7 @@
 
 You don't need to tune the parameters of strelka. It bases on [trained models](<https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/trainingGermlineEmpiricalScore.md>), you may train new models to improve performance.
 
-Why?
+
 
 
 
@@ -20,9 +20,11 @@ Two steps:
    
    ```
 
+##### Per sample run time
 
+4h30min
 
 ##### Reference
 
 1. Strelka User Guide <https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md>
-2. 
+2. Strelka paper <https://www.nature.com/articles/s41592-018-0051-x>

tasks/strelka.wdl

@@ -2,7 +2,6 @@ task strelka {
 
     File ref_dir
 	File fasta
-
 	File Dedup_bam
 	File Dedup_bam_index
 	String sample
@@ -16,6 +15,7 @@ task strelka {
 		nt=$(nproc)
 		/strelka-2.9.10.centos6_x86_64/bin/configureStrelkaGermlineWorkflow.py --bam ${Dedup_bam} --referenceFasta ${ref_dir}/${fasta} 
 		StrelkaGermlineWorkflow/runWorkflow.py -m local -j $nt
+		mv StrelkaGermlineWorkflow/results/variants/variants.vcf.gz StrelkaGermlineWorkflow/results/variants/${sample}_strelka2.vcf.gz 
 	>>>
 
 	runtime {
@@ -25,6 +25,6 @@ task strelka {
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		Array[File] output_files = glob("StrelkaGermlineWorkflow/results/variants/*")
+		File strelka_vcf = "StrelkaGermlineWorkflow/results/variants/${sample}_strelka2.vcf.gz"
 	}
 }