更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -22,6 +22,10 @@ task cnvkit{
        nt=$(nproc)
         
        echo ${sample}
+       
+       center=`awk -v vv=${center_at} 'BEGIN {print log(2/vv)/log(2)}'`
+       
+       echo $center         
 
        if [ ${normal_bam} ]; then   
                /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
@@ -54,7 +58,7 @@ task cnvkit{
                   -p $nt
                   
        ls ./
-       /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at ${center_at} \
+       /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \
                   -o ${sample}.call.cns