更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -32,12 +32,17 @@ task cnvkit{
                   --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 
+               /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed
+    	       # Prepare the target bed
+               /root/miniconda2/bin/cnvkit.py --annotate ${ref_flat} --split --short-names -o my_baits.bed
+               
+               /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} -t my_baits.bed -g access.bed
+               
+               /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn
+               /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} my_baits.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn
+                  
+               /root/miniconda2/bin/cnvkit.py reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t my_baits.target.bed -a my_baits.antitarget.bed
+                  
        fi
                   
        ls ./