From 157fa94ef886218af47d857b64f5a3625f365b0f Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Mon, 26 Feb 2024 10:05:47 +0800
Subject: [PATCH] =?UTF-8?q?=E6=B1=A1=E6=9F=93=E6=B7=BB=E5=8A=A017=E5=92=8C?=
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---
 codes/pollution.py |  6 ++++++
 wdl/pollution.wdl  | 23 +++++++++++++++++++++++
 2 files changed, 29 insertions(+)

diff --git a/codes/pollution.py b/codes/pollution.py
index 1674529..69b58f5 100755
--- a/codes/pollution.py
+++ b/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
diff --git a/wdl/pollution.wdl b/wdl/pollution.wdl
index 3f2e6bd..4c3a569 100755
--- a/wdl/pollution.wdl
+++ b/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
+
+            }
         }
     }