alter 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
-            cp ${bed} access-mappable.bed
+            touch access-mappable.bed
         else
             cnvkit.py access -s ${min_gap_size} -o access-mappable.bed ${fasta}
         fi

tasks/batch.wdl

 
     String annotate_opt = if (ref_flat != "") then "--annotate ${ref_flat}" else ""
     String reference_opt = if (reference != "") then "--reference ${reference}" else ""
+    String access_opt = if (method == "amplicon") then "--access ${bed}" else "--access ${access_bed}"
 
     command <<<
         set -o pipefail
         
         mkdir results
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
-        --targets ${bed} --method ${method} \
-        ${annotate_opt} ${reference_opt} \
-        --fasta hg38.fa --access ${access_bed} \
+        --method ${method} \
+        --targets ${bed} ${annotate_opt} \
+        --fasta hg38.fa ${access_opt} ${reference_opt} \
         --output-reference ~/${sample_id}.reference.cnn \
         --output-dir ./results/ \
         --drop-low-coverage --diagram --scatter

workflow.wdl

         faidx = faidx,
         method = method,
         min_gap_size = min_gap_size,
-        bed = bed,
         docker = docker,
         cluster_config = cluster_config,
         disk_size = disk_size