alter batch.wdl

tasks/access.wdl

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

tasks/batch.wdl

     Array[File] tumor_bai
     Array[File] normal_bam
     Array[File] normal_bai
-    File? bed
+    File bed
     File faidx
     File fasta
     File? ref_flat
         cp ${faidx} /cromwell_root/tmp/cnvkit/hg38.fai
         cp ${access_bed} /cromwell_root/tmp/cnvkit/access-mappable.bed
         # optional parameters
-        if [ ${bed} != "" ]; then cp ${bed} /cromwell_root/tmp/cnvkit/amplicon.bed; fi
+        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
         mkdir results
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --method ${method} --segment-method ${segment_method} \
-        --targets amplicon.bed ${access_opt} ${annotate_opt} \
+        --targets ${bed} ${access_opt} ${annotate_opt} \
         --fasta hg38.fa ${reference_opt} \
         --output-reference ${sample_id}.reference.cnn \
         --output-dir ./results/ \

workflow.wdl

     Array[File] tumor_bai
     Array[File] normal_bam
     Array[File] normal_bai
-    File? bed
+    File bed
 	File faidx
 	File fasta
     File? ref_flat