alter batch output

tasks/batch.wdl

@@ -18,7 +18,7 @@ task batch {
 
     String annotate_opt = if (ref_flat != "") then "--annotate ref_flat.txt" else ""
     String reference_opt = if (reference != "") then "--reference my_reference.cnn" else ""
-    String access_opt = if (method == "amplicon") then "--access amplicon.bed" else "--access access-mappable.bed"
+    String access_opt = if (method == "amplicon") then "--access target.bed" else "--access access-mappable.bed"
 
     command <<<
         set -o pipefail
@@ -29,21 +29,23 @@ task batch {
         # must exist parameters
         cp ${fasta} /cromwell_root/tmp/cnvkit/hg38.fa
         cp ${faidx} /cromwell_root/tmp/cnvkit/hg38.fai
+        cp ${bed} /cromwell_root/tmp/cnvkit/target.bed
         cp ${access_bed} /cromwell_root/tmp/cnvkit/access-mappable.bed
         # optional parameters
-        if [ ${method} == "amplicon" ]; then cp ${bed} /cromwell_root/tmp/cnvkit/amplicon.bed; fi
         if [ ${ref_flat} != "" ]; then cp ${ref_flat} /cromwell_root/tmp/cnvkit/ref_flat.txt; fi
         if [ ${reference} != "" ]; then cp ${reference} /cromwell_root/tmp/cnvkit/my_reference.cnn; fi
-        cd /cromwell_root/tmp/cnvkit
         
+        cd /cromwell_root/tmp/cnvkit
         mkdir results
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --method ${method} --segment-method ${segment_method} \
-        --targets ${bed} ${access_opt} ${annotate_opt} \
+        --targets target.bed ${access_opt} ${annotate_opt} \
         --fasta hg38.fa ${reference_opt} \
         --output-reference ${sample_id}.reference.cnn \
         --output-dir ./results/ \
         --drop-low-coverage --diagram --scatter
+        
+        cp ${sample_id}.reference.cnn ~/${sample_id}.reference.cnn
     >>>
 
     runtime {