修改脚本错误更新README.md

README.md

@@ -21,14 +21,14 @@ choppy install XXXX
 
 ### 甲基化原理简述
 
+![](.\picture\BS原理.png)
+
 全基因组亚硫酸氢盐测序用于研究基因粒度的DNA甲基化模式。 亚硫酸氢盐处理将胞嘧啶转化为尿嘧啶，但甲基化胞嘧啶不变。
 
 比对软件（如Bismark）将基因组序列转化之后进行比对。
 
 
 
-![img](file:///C:/Users/monster/Documents/My Knowledge/temp/bbfd4716-e9eb-4735-9f7c-948838adbb62/128/index_files/004e3e03-4e75-487f-8be6-fa7509f07930.png)
-
 ### APP功能简述
 
 为了更好的分析全基因组甲基化数据，我们选用了目前最好的比对软件Bismark，构建了分析pipeline。用来提取全基因组的CpG，CHH,CHG甲基化模式信息。
@@ -37,7 +37,9 @@ choppy install XXXX
 
 ### WGBS分析流程
 
-  ![img](file:///C:/Users/monster/Documents/My Knowledge/temp/bbfd4716-e9eb-4735-9f7c-948838adbb62/128/index_files/c5901b21-4df4-46c4-a68a-11cb11476af7.png)
+
+
+![](.\picture\WGBS流程.png)
 
 ### 参数说明      
 
@@ -57,6 +59,8 @@ choppy install XXXX
 
 -p 多线程
 
+```
+
 
 
 ## 输入和输出
@@ -80,13 +84,11 @@ CpG_context_test_data_bismark_bt2.txt，CHG_context_test_data_bismark_bt2.txt，
 以CpG_context_test_data_bismark_bt2.txt为例
 
 ```
-
 Bismark methylation extractor version v0.19.0
 SRR15024317_length=86   -       1       57798691        z
 SRR15024319_length=86    +       2       10166600        Z
 SRR15024331_length=86  +       11      77736289        Z
 SRR15024338_length=86  +       3       197272186       Z
-
 ```
 
 第一行为Bismark的版本信息
@@ -96,7 +98,6 @@ SRR15024338_length=86  +       3       197272186       Z
 不同字母表明不同的甲基化状态：
 
 ```
-
 X 代表CHG中甲基化的C
 x  代笔CHG中非甲基化的C
 H 代表CHH中甲基化的C
@@ -105,31 +106,21 @@ Z  代表CpG中甲基化的C
 z  代表CpG中非甲基化的C
 U 代表其他情况的甲基化C(CN或者CHN)
 u  代表其他情况的非甲基化C (CN或者CHN)
-
 ```
 
 #### 补充文件
 
 上面的文件是methylation calling 最直接的证据，但是对于甲基化水平的定量来说，缺少了相关信息。运行bismark_methylation_extractor时，除了生成上述文件之外，还会有下列3个文件：
 
-```
-
 test_data_bismark_bt2_splitting_report.txt
 test_data_bismark_bt2.M-bias.txt
 test_data_bismark_bt2.M-bias_R1.png
 
-
-
-```
-
-
-
 ##### test_data_bismark_bt2_splitting_report.txt
 
 记录了该样本甲基化的汇总信息
 
 ```
-
 Final Cytosine Methylation Report
 Total number of C’s analysed:    40348
 Total methylated C’s in CpG context:    1365
@@ -141,7 +132,6 @@ Total C to T conversions in CHH context:    28105
 C methylated in CpG context:    66.8%
 C methylated in CHG context:    0.2%
 C methylated in CHH context:    0.4%
-
 ```
 
 ##### test_data_bismark_bt2.M-bias.txt
@@ -150,12 +140,10 @@ C methylated in CHH context:    0.4%
 部分文件内容如下
 
 ```
-
 CpG context
 position        count methylated        count unmethylated      % methylation   coverage
 1                     42                         13               76.36         55
 2                     31                          9               77.50         40
-
 ```
 
 

inputs

@@ -1,12 +1,10 @@
 {
-  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
-  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "{{ project_name }}.ref_dir": "oss://pgx-test-data/wgbs/genome/hg38/",
   "{{ project_name }}.fastq_1": "{{ read1 }}",
   "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn2ne.2xlarge img-ubuntu-vpc' }}",
-  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bismark",
   "{{ project_name }}.sample": "{{ sample_name }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}", 
-  "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.fastq_2": "{{ read2 }}"
 }
 

tasks/Dedup.wdl

@@ -12,7 +12,6 @@ task Dedup {
 	command <<<
 		set -o pipefail
 		set -e
-		nt=$(nproc)
 		deduplicate_bismark -p --bam ${unsorted_bam}	
 	>>>
 	runtime {

tasks/Dedup.wdl.bak

@@ -0,0 +1,34 @@
+task Dedup {
+
+	String sample
+
+	File unsorted_bam
+
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		deduplicate_bismark -p --bam ${unsorted_bam}	
+	>>>
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File Dedup_bam = "${sample}_R1_val_1_bismark_bt2_pe.deduplicated.bam"
+	}
+}
+
+
+
+
+
+

tasks/Mapping.wdl

@@ -12,8 +12,7 @@ task mapping {
 	command <<<
 		set -o pipefail
 		set -e	
-		nt=$(nproc)
-		bismark --bowtie2 -p ${nt} --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
+		bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
 
 	>>>
 

tasks/Mapping.wdl.bak

@@ -0,0 +1,29 @@
+task mapping {
+
+    File ref_dir
+	File trim_read1
+	File trim_read2
+
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e	
+		nt=$(nproc)
+		bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
+
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File unsorted_bam = "${sample}_R1_val_1_bismark_bt2_pe.bam"
+	}
+}