更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -5,6 +5,7 @@ task cnvkit{
     String? fasta
     File ref_flat
     File bed_file
+    String method
     File hrd
     File tumor_bam
     File tumor_bam_index
@@ -23,7 +24,10 @@ task cnvkit{
         
        echo ${sample}
                   
+                  
        PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
+                  
+       echo $PURITY
        
        center=`awk -v vv=$PURITY 'BEGIN {print log(2/vv)/log(2)}'`
        
@@ -32,7 +36,7 @@ task cnvkit{
        if [ ${normal_bam} ]; then   
                /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
                   --normal ${normal_bam} \
-                  --method wgs \
+                  --method ${method} \
                   --fasta ${ref_dir} \
                   --annotate ${ref_flat} -p $nt \
                   --drop-low-coverage \
@@ -42,7 +46,7 @@ task cnvkit{
     	       # 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} --method wgs -g access.bed
+               /root/miniconda2/bin/cnvkit.py autobin ${tumor_bam} --method ${method} -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