first commit

inputs

@@ -10,7 +10,7 @@
   "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
   "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
   "{{ project_name }}.db_mills": "{{ db_mills }}",
-  "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
+  "{{ project_name }}.muse_docker": "{{ muse_docker }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
   "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",

tasks/muse.wdl

@@ -16,7 +16,7 @@ task muse {
 
     command <<<
         ./MuSE call –O ${sample} –f ${ref_dir}/${fasta} ${tumor_bam} ${normal_bam}
-        ./MuSE sump -I ${sample}.MuSE.txt -E –O ${sample}.MuSE.TN.vcf –D 
+        ./MuSE sump -I ${sample}.MuSE.txt -E –O ${sample}.MuSE.TN.vcf –D ${dbsnp_dir}/${dbsnp}
     >>>
 
     runtime {