hg38 to hg_ref

tasks/batch.wdl

@@ -26,8 +26,8 @@ task batch {
         mkdir -p /cromwell_root/tmp/cnvkit
 
         # must exist parameters
-        cp ${fasta} /cromwell_root/tmp/cnvkit/hg38.fa
-        cp ${faidx} /cromwell_root/tmp/cnvkit/hg38.fai
+        cp ${fasta} /cromwell_root/tmp/cnvkit/hg_ref.fa
+        cp ${faidx} /cromwell_root/tmp/cnvkit/hg_ref.fai
         cp ${bed} /cromwell_root/tmp/cnvkit/target.bed
         cp ${access_bed} /cromwell_root/tmp/cnvkit/access-mappable.bed
 
@@ -40,7 +40,7 @@ task batch {
         cnvkit.py batch -p $nt ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --method ${method} --segment-method ${segment_method} \
         --targets target.bed ${access_opt} ${annotate_opt} \
-        --fasta hg38.fa ${reference_opt} \
+        --fasta hg_ref.fa ${reference_opt} \
         --output-reference ${sample_id}.reference.cnn \
         --output-dir ./results/ \
         --drop-low-coverage --diagram --scatter

workflow.wdl

@@ -7,8 +7,8 @@ workflow {{ project_name }} {
     Array[File] tumor_bam
     Array[File] normal_bam
     File bed
-	File faidx
-	File fasta
+    File faidx
+    File fasta
     File? ref_flat
     File? reference
     String min_gap_size