add --no-rebuild and --faidx

tasks/batch.wdl

@@ -22,8 +22,8 @@ task batch {
         cd /cromwell_root/tmp/cnvkit
         
         mkdir results
-        cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
-        --targets ${bed} --faidx --no-rebuild --annotate ${ref_flat} \
+        cnvkit.py batch faidx --no-rebuild${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
+        --targets ${bed} --annotate ${ref_flat} \
         --fasta ${ref_dir}/${fasta} --access ${access_bed} \
         --output-reference ${sample_id}.reference.cnn --output-dir /cromwell_root/tmp/cnvkit/results/ \
         --diagram --scatter