fix(CNVkit): version 0.9.9

defaults

@@ -26,7 +26,7 @@
   "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/bcftools:v1.9",
   "annovar_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annovar:v20191024",
   "annotsv_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annotsv:3.1.3",
-  "cnvkit_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/cnvkit:0.9.8",
+  "cnvkit_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/cnvkit:0.9.9",
   "sequenza_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sequenza:3.0.0",
   "msisensor_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/msisensor-pro:1.2.0",
   "tmb_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/tmb:1.0.0",

tasks/CNVkit.wdl

@@ -66,9 +66,11 @@ task CNVkit {
     cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt
     cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt
     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
+      cnvkit.py scatter ${sample}.call.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf || echo $gene >> failed_genes.txt
     done
   >>>
   
@@ -90,7 +92,8 @@ task CNVkit {
     File call_cns = "${sample}.call.cns"
     File ratio_cnv = "${sample}.ratio_cnv.txt"
     File segment_cnv = "${sample}.segment_cnv.txt"
-    File gainloss_genes = "${sample}.trusted_genes.txt"
+    File trusted_genes = "${sample}.trusted_genes.txt"
+    File failed_genes = "${sample}.failed_genes.txt"
     Array[File] gainloss = glob("./gainloss/*")
   }
 }