test --no-rebuild

tasks/batch.wdl

@@ -19,13 +19,14 @@ task batch {
         mkdir -p /cromwell_root/tmp/cnvkit
         cp ${sep=' ' normal_bai} /cromwell_root/tmp/cnvkit
         cp ${sep=' ' tumor_bai} /cromwell_root/tmp/cnvkit
-        cp ${faidx} /cromwell_root/tmp/cnvkit
+        ln ${fasta} /cromwell_root/tmp/cnvkit/hg38.fa
+        ln ${faidx} /cromwell_root/tmp/cnvkit/hg38.fai
         cd /cromwell_root/tmp/cnvkit
         
         mkdir results
         cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --targets ${bed} --annotate ${ref_flat} \
-        --fasta ${fasta} --no-rebuild ${faidx} --access ${access_bed} \
+        --fasta hg38.fa --access ${access_bed} \
         --output-reference ${sample_id}.reference.cnn --output-dir /cromwell_root/tmp/cnvkit/results/ \
         --diagram --scatter
     >>>