aler batch.wdl

tasks/batch.wdl

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