更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -4,7 +4,7 @@ task cnvkit{
     File ref_dir
     String? fasta
     File ref_flat
-    File bed_file
+    File? bed_file
     File hrd
     File tumor_bam
     File tumor_bam_index
@@ -30,28 +30,56 @@ task cnvkit{
        
        center=`awk -v vv=$Ploidy 'BEGIN {print log(2/vv)/log(2)}'`
        
-       echo $center         
-
-       if [ ${normal_bam} ]; then   
-               /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
-                  --normal ${normal_bam} \
-                  --method wgs \
-                  --fasta ${ref_dir} \
-                  --annotate ${ref_flat} -p $nt \
-                  --drop-low-coverage \
-                  --output-dir ${sample}.reference.cnn
-       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 autobin ${tumor_bam} --method wgs -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 reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t ${sample}.target.bed -a ${sample}.antitarget.bed
+       echo $center 
                   
+       #WES
+       if [ ${bed_file} ]; then
+           if [ ${normal_bam} ]; then
+                   /root/miniconda2/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed
+                   /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
+                      --normal ${normal_bam} \
+                      --targets my_baits.bed \
+                      --fasta ${ref_dir} \
+                      --annotate ${ref_flat} -p $nt \
+                      --drop-low-coverage \
+                      --output-dir ${sample}.reference.cnn
+           else
+                   /root/miniconda2/bin/cnvkit.py access ${ref_dir} -o access.bed
+                   # Prepare the target bed
+                  /root/miniconda2/bin/cnvkit.py target ${bed_file} --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} ${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 reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t ${sample}.target.bed -a ${sample}.antitarget.bed
+           fi
+    
+       #WGS         
+       else:
+
+           if [ ${normal_bam} ]; then   
+                   /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
+                      --normal ${normal_bam} \
+                      --method wgs \
+                      --fasta ${ref_dir} \
+                      --annotate ${ref_flat} -p $nt \
+                      --drop-low-coverage \
+                      --output-dir ${sample}.reference.cnn
+           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 autobin ${tumor_bam} --method wgs -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 reference -o ${sample}.reference.cnn/reference.cnn -f ${ref_dir} -t ${sample}.target.bed -a ${sample}.antitarget.bed
+
+           fi
        fi
                   
        ls ./