更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -34,9 +34,9 @@ task cnvkit{
        else
                /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 --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 autobin ${tumor_bam} -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