test

tasks/batch.wdl

@@ -19,8 +19,8 @@ task batch {
         mkdir -p /cromwell_root/tmp/cnvkit
         cp ${sep=' ' normal_bai} /cromwell_root/tmp/cnvkit
         cp ${sep=' ' tumor_bai} /cromwell_root/tmp/cnvkit
-        ln ${fasta} /cromwell_root/tmp/cnvkit/hg38.fa
-        ln ${faidx} /cromwell_root/tmp/cnvkit/hg38.fai
+        cp ${fasta} /cromwell_root/tmp/cnvkit/hg38.fa
+        cp ${faidx} /cromwell_root/tmp/cnvkit/hg38.fai
         cd /cromwell_root/tmp/cnvkit
         
         mkdir results