更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -50,10 +50,10 @@ task cnvkit{
 
                    /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} -t my_baits.bed -g access.bed
 
-                   /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.target.bed -o ${sample}.T.targetcoverage.cnn
-                   /root/miniconda2/bin/cnvkit.py coverage ${tumor_bam} ${sample}.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn
+                   /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 ${sample}.target.bed -a ${sample}.antitarget.bed
+                   /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
     
        #WGS