test(CNVkit): pause plot

tasks/CNVkit.wdl

     comm -12 ratio_cnv.txt segment_cnv.txt > ${sample}.trusted_genes.txt
     # Scatter plot for each gene
     touch failed_genes.txt
-    for gene in `cat ${sample}.trusted_genes.txt`
-    do
-      cnvkit.py scatter ${sample}.call.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf || echo $gene >> failed_genes.txt
-    done
+    # for gene in `cat ${sample}.trusted_genes.txt`
+    # do
+    #   cnvkit.py scatter ${sample}.call.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf || echo $gene >> failed_genes.txt
+    # done
   >>>
   
   runtime {