添加 'tasks/CNVkit_multi_REF'

tasks/CNVkit_multi_REF

@@ -0,0 +1,84 @@
+task cnvkit{
+    String sample_id
+    File ref_dir
+    String? fasta
+    File ref_flat
+    File? bed_file
+    String? Ploidy
+    File tumor_bam
+    File tumor_bam_index
+    Array[File]? normal_bams
+    Array[File]? normal_bam_indexs
+    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 ${sep=" " normal_bams}
+                  
+                  
+       echo ${Ploidy}
+       
+       center=`awk -v vv=${Ploidy} 'BEGIN {print log(2/vv)/log(2)}'`
+       
+       echo $center 
+
+       /usr/local/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed
+                  /usr/local/bin/cnvkit.py batch ${tumor_bam} \
+                  --normal ${sep=" " normal_bams} \
+                  --targets my_baits.bed \
+                  --fasta ${ref_dir} \
+                  --annotate ${ref_flat} -p $nt \
+                  --drop-low-coverage \
+                  --output-dir ${sample}.reference.cnn
+                  
+                                    
+       ls ./
+       
+        
+       /usr/local/bin/cnvkit.py batch  ${tumor_bam} \
+                  -r ${sample}.reference.cnn/reference.cnn \
+                  --output-dir ${sample}.cns \
+                  -p $nt
+                  
+       ls ./
+       /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \
+                  -o ${sample}.call.cns
+                  
+       
+           # Plot the results
+    	/usr/local/bin/cnvkit.py scatter ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
+    	/usr/local/bin/cnvkit.py diagram ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
+    	/usr/local/bin/cnvkit.py heatmap ${sample}.cns/${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
+       
+         
+        #gain and loss
+        /usr/local/bin/cnvkit.py export vcf ${sample}.call.cns -y -i "${sample}" -o ${sample}.call.cns.vcf
+                
+
+        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}.call.cns.vcf"
+    }
+
+}