fix bug: the timestamp of BED files

tasks/batch.wdl

@@ -4,7 +4,7 @@ task batch {
     Array[File] tumor_bai
     Array[File] normal_bam
     Array[File] normal_bai
-    File bed
+    File? bed
     File faidx
     File fasta
     File? ref_flat
@@ -15,9 +15,9 @@ task batch {
     String cluster_config
     String disk_size
 
-    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}"
+    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"
 
     command <<<
         set -o pipefail
@@ -25,15 +25,21 @@ task batch {
         mkdir -p /cromwell_root/tmp/cnvkit
         cp ${sep=' ' normal_bai} /cromwell_root/tmp/cnvkit
         cp ${sep=' ' tumor_bai} /cromwell_root/tmp/cnvkit
+        # must exist parameters
         cp ${fasta} /cromwell_root/tmp/cnvkit/hg38.fa
         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 [ ${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} \
-        --targets ${bed} ${annotate_opt} \
-        --fasta hg38.fa ${access_opt} ${reference_opt} \
+        --targets amplicon.bed ${access_opt} ${annotate_opt} \
+        --fasta hg38.fa ${reference_opt} \
         --output-reference ~/${sample_id}.reference.cnn \
         --output-dir ./results/ \
         --drop-low-coverage --diagram --scatter

workflow.wdl

@@ -8,7 +8,7 @@ workflow {{ project_name }} {
     Array[File] tumor_bai
     Array[File] normal_bam
     Array[File] normal_bai
-    File bed
+    File? bed
 	File faidx
 	File fasta
     File? ref_flat