alter format access

tasks/access.wdl

 task access {
     File faidx
     File fasta
+    File? bed
     String method
     String min_gap_size
     String docker
 
     command <<<
         if [ ${method}=="amplicon" ]; then
-            touch access-mappable.bed
+            cp ${bed} access-mappable.bed
         else
             cnvkit.py access -s ${min_gap_size} -o access-mappable.bed ${fasta}
         fi

workflow.wdl

         input: 
         fasta = fasta,
         faidx = faidx,
+        bed = bed,
         method = method,
         min_gap_size = min_gap_size,
         docker = docker,