update

cn.mops.R

 #2 Set up
 #
 ##2.1 load package
-library(cn.mops)
+library(cn.mops) #cn.mops_1.16.2
 #
 ##2.2 load options
 #
 	  --TumorSampleID=the name of the TUMOR sample  - string
       --bed_file=BED (Browser Extensible Data) lines have four required fields included chr, start, end and gene annotation.  - string
       --workDir=working directory   - character
-      --outputDir=where you want to output the pictures - character
       --help              - print this text
       
       
       Example:
-      Rscript cn.mops.R --Tumor=TumorSample.bam --Normal=NormalSample.bam --TumorSampleID=TumorSampleID --bed_file=bedFile --workDir=./ --outputDir=./ \n\n")
+      Rscript cn.mops.R --Tumor=TumorSample.bam --Normal=NormalSample.bam --TumorSampleID=TumorSampleID --bed_file=bedFile --workDir=./ \n\n") #--outputDir=./ 
   
   q(save="no")
 }
   workDir=args$workDir
 }
 #
-## Arg6 default
-if(is.null(args$outputDir)) {
-  stop("outputDir is missing")
-}else{
-  outputDir=args$outputDir
-}
-#
 #3 Run cn.mops
 # Tumor <- c("Illumina_pt2_B1700.chr20_X.sorted.deduped.bam")
 # Normal <- c("Illumina_pt2_B17NC.chr20_X.sorted.deduped.bam")
                   CN=Res$CN)
 #
 ##3.4 Output
-write.table(Res,paste0(outputDir,"/",TumorSampleID,"cn.mops.res.txt"),sep="\t",
+write.table(Res,paste0(TumorSampleID,"cn.mops.res.txt"),sep="\t",
            col.names=T,row.names=F,quote=F)
 
 

inputs

 {
   "{{ project_name }}.TumorBam": "{{ TumorBam }}",
   "{{ project_name }}.TumorSampleID": "{{ TumorSampleID }}",
-  "{{ project_name }}.outputDir": "{{ outputDir }}",
   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
   "{{ project_name }}.workDir": "{{ workDir }}",

tasks/cn_mops.wdl

 	String TumorSampleID
 	String bed_file
 	String workDir
-	String outputDir
 	String docker
 	String disk_size
 	String cluster_config
 	
 	command <<<
-		Rscript cn.mops.R --Tumor=${TumorBam} --Normal=${NormalBam} --TumorID==${TumorSampleID} --bed_file=${bed_file} --workDir=${workDir} --outputDir=${outputDir}
+		Rscript cn.mops.R --Tumor=${TumorBam} --Normal=${NormalBam} --TumorID==${TumorSampleID} --bed_file=${bed_file} --workDir=${workDir}
 	>>>
 
 	runtime {

workflow.wdl

 	String TumorSampleID
 	String bed_file
 	String workDir
-	String outputDir
 	String docker
 	String disk_size
 	String cluster_config
 			TumorSampleID=TumorSampleID,
 			bed_file=bed_file,
 			workDir=workDir,
-			outputDir=outputDir,
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config