污染添加17和160图

codes/pollution.py

@@ -46,9 +46,13 @@ def single_monitor(name, vcf_file, bed_file, freq_range, output_dir):
     bed_regions = load_bed_regions(bed_file)
 
     vcf = pysam.VariantFile(vcf_file)
+
     res_pos = list()
     count_normal = 0
     count_exception = 0
+    vcf_out = open(os.path.join(output_dir, f'{name}_cnvkit_tumor.vcf'), 'w')
+    for line in str(vcf.header).strip().split('\n'):
+        vcf_out.write(line + '\n')
 
     for record in vcf:
         contig = record.contig
@@ -79,7 +83,9 @@ def single_monitor(name, vcf_file, bed_file, freq_range, output_dir):
                         freq=freq,
                         res=res
                     ))
+                    vcf_out.write(str(record) + '\n')
                     break
+
     count_all = count_exception + count_normal
     if count_all == 0:
         z_score = 0

wdl/pollution.wdl

@@ -61,6 +61,19 @@ task run_generate_png {
     }
 }
 
+task run_single_generate_png {
+    String name
+    String probe
+    String cnvkit_tumor_vcf
+    String cnv_cnr
+    String cnv_cns
+    String output_dir
+
+    command {
+        cnvkit.py scatter ${cnv_cnr} -s ${cnv_cns} -v ${cnvkit_tumor_vcf} -o ${output_dir}/pollution/${name}_pollution_cnvkit_tumor.png
+    }
+}
+
 workflow call_pollution {
 
     Boolean run=true
@@ -114,6 +127,16 @@ workflow call_pollution {
                     probe=probe,
                     vcf=initial_vcf
             }
+            call run_single_generate_png {
+                input:
+                    name=tumor,
+                    probe=probe,
+                    cnvkit_tumor_vcf=run_pollution_paired.cnvkit_tumor_vcf,
+                    cnv_cnr=cnv_cnr,
+                    cnv_cns=cnv_cns,
+                    output_dir=output_dir
+
+            }
         }
     }