更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -16,20 +16,29 @@ task cnvkit{
 
     command <<<
 
-        set -o pipefail
-        set -e
-        nt=$(nproc)
+       set -o pipefail
+       set -e
+       nt=$(nproc)
         
-        echo ${sample}
+       echo ${sample}
 
-        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
+       if [ ${normal_bam} ]; then   
+               /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
                   --normal ${normal_bam} \
                   --method wgs \
                   --fasta ${ref_dir} \
                   --annotate ${ref_flat} -p $nt \
-                  --targets ${bed_file} \
                   --drop-low-coverage \
                   --output-dir ${sample}.reference.cnn
+       else
+               /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
+                  --method wgs \
+                  --fasta ${ref_dir} \
+                  --annotate ${ref_flat} -p $nt \
+                  --drop-low-coverage \
+                  --output-dir ${sample}.reference.cnn 
+       fi
+                  
        ls ./