添加 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -0,0 +1,115 @@
+task cnvkit{
+    String sample_id
+    File ref_dir
+    String? fasta
+    File ref_flat
+    File? bed_file
+    String? Polidy
+    File tumor_bam
+    File tumor_bam_index
+    File? normal_bam
+    File? normal_bam_index
+    String docker
+    String cluster_config
+    String disk_size
+    String sample=basename(tumor_bam,".bam")
+
+    command <<<
+
+       set -o pipefail
+       set -e
+       nt=$(nproc)
+        
+       echo ${sample}
+                  
+                  
+       echo ${Ploidy}
+       
+       center=`awk -v vv=${Ploidy} 'BEGIN {print log(2/vv)/log(2)}'`
+       
+       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 ./
+       
+        
+       /root/miniconda2/bin/cnvkit.py batch  ${tumor_bam} \
+                  -r ${sample}.reference.cnn/reference.cnn \
+                  --output-dir ${sample}.cns \
+                  -p $nt
+                  
+       ls ./
+       /root/miniconda2/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \
+                  -o ${sample}.call.cns
+                  
+                
+
+        ls ./
+
+        tar cvf ${sample}.tar ${sample}*
+
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+        timeout:259200
+    }
+
+    output{
+        File out_file = "${sample}.tar"
+        #File cnv_bed = "${sample}.ratio_cnv.call.filter.bed"
+    }
+
+}