From 5cffa788d062746134a16de7b86bde7ebc532afa Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Tue, 29 Aug 2023 10:42:42 +0800
Subject: [PATCH] =?UTF-8?q?=E6=B7=BB=E5=8A=A0dot=20=E6=B5=81=E7=A8=8B?=
 =?UTF-8?q?=E5=9B=BE?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 README.md          |  15 ++--
 other/pipelie.svg  | 172 +++++++++++++++++++++++++++++++++++++++++++++
 other/pipeline.dot |   8 +--
 3 files changed, 187 insertions(+), 8 deletions(-)
 create mode 100644 other/pipelie.svg

diff --git a/README.md b/README.md
index 0b729ac..cc44e19 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,15 @@
 
 ## run script example 
 ```bash
-java -Dconfig.file=/home/zhangchao/project/pipeline/wdl/cromwell.examples.conf \
+/home/zhangchao/soft/jdk-17.0.7+7/bin/java -Dconfig.file=/home/zhangchao/project/pipeline/wdl/cromwell.examples.conf \
 -jar /home/zhangchao/soft/cromwell-85.jar run  \
---inputs ~/project/pipeline/workflow/test/20230814.json \
-~/project/pipeline/workflow/pipeline.wdl
-```
\ No newline at end of file
+--inputs /home/zhangchao/project/pipeline/workflow/test/20230814.json \
+/home/zhangchao/project/pipeline/workflow/pipeline.wdl
+```
+
+## dot 
+```bash
+womtool graph pipeline.wdl > other/pipeline.dot
+```
+
+![流程图](./other/pipelie.svg)
diff --git a/other/pipelie.svg b/other/pipelie.svg
new file mode 100644
index 0000000..22eb24b
--- /dev/null
+++ b/other/pipelie.svg
@@ -0,0 +1,172 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 8.1.0 (20230707.0739)
+ -->
+<!-- Title: pipeline Pages: 1 -->
+<svg width="797pt" height="356pt"
+ viewBox="0.00 0.00 797.25 356.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 352)">
+<title>pipeline</title>
+<polygon fill="white" stroke="none" points="-4,4 -4,-352 793.25,-352 793.25,4 -4,4"/>
+<!-- CALL_mutation_calling -->
+<g id="node1" class="node">
+<title>CALL_mutation_calling</title>
+<ellipse fill="none" stroke="black" cx="565.55" cy="-166" rx="85.99" ry="18"/>
+<text text-anchor="middle" x="565.55" y="-160.57" font-family="Times New Roman,serif" font-size="14.00">call mutation_calling</text>
+</g>
+<!-- CALL_neoantigen -->
+<g id="node2" class="node">
+<title>CALL_neoantigen</title>
+<ellipse fill="none" stroke="black" cx="254.55" cy="-90" rx="65.04" ry="18"/>
+<text text-anchor="middle" x="254.55" y="-84.58" font-family="Times New Roman,serif" font-size="14.00">call neoantigen</text>
+</g>
+<!-- CALL_mutation_calling&#45;&gt;CALL_neoantigen -->
+<g id="edge1" class="edge">
+<title>CALL_mutation_calling&#45;&gt;CALL_neoantigen</title>
+<path fill="none" stroke="black" d="M510.31,-151.86C454.88,-138.67 369.83,-118.43 313.22,-104.96"/>
+<polygon fill="black" stroke="black" points="314.19,-101.35 303.65,-102.44 312.57,-108.16 314.19,-101.35"/>
+</g>
+<!-- CALL_annovar -->
+<g id="node9" class="node">
+<title>CALL_annovar</title>
+<ellipse fill="none" stroke="black" cx="682.55" cy="-90" rx="55.06" ry="18"/>
+<text text-anchor="middle" x="682.55" y="-84.58" font-family="Times New Roman,serif" font-size="14.00">call annovar</text>
+</g>
+<!-- CALL_mutation_calling&#45;&gt;CALL_annovar -->
+<g id="edge9" class="edge">
+<title>CALL_mutation_calling&#45;&gt;CALL_annovar</title>
+<path fill="none" stroke="black" d="M591.81,-148.39C608.68,-137.72 630.74,-123.77 648.89,-112.29"/>
+<polygon fill="black" stroke="black" points="650.4,-114.84 656.98,-106.54 646.66,-108.93 650.4,-114.84"/>
+</g>
+<!-- CALL_statistics -->
+<g id="node3" class="node">
+<title>CALL_statistics</title>
+<ellipse fill="none" stroke="black" cx="61.55" cy="-166" rx="57.55" ry="18"/>
+<ellipse fill="none" stroke="black" cx="61.55" cy="-166" rx="61.55" ry="22"/>
+<text text-anchor="middle" x="61.55" y="-160.57" font-family="Times New Roman,serif" font-size="14.00">call statistics</text>
+</g>
+<!-- CALL_fusion -->
+<g id="node4" class="node">
+<title>CALL_fusion</title>
+<ellipse fill="none" stroke="black" cx="111.55" cy="-90" rx="48.57" ry="18"/>
+<text text-anchor="middle" x="111.55" y="-84.58" font-family="Times New Roman,serif" font-size="14.00">call fusion</text>
+</g>
+<!-- CALL_statistics&#45;&gt;CALL_fusion -->
+<g id="edge2" class="edge">
+<title>CALL_statistics&#45;&gt;CALL_fusion</title>
+<path fill="none" stroke="black" d="M75.48,-144.39C81.31,-135.75 88.15,-125.63 94.3,-116.53"/>
+<polygon fill="black" stroke="black" points="97.69,-118.77 100.38,-108.53 91.89,-114.85 97.69,-118.77"/>
+</g>
+<!-- CALL_alignment -->
+<g id="node5" class="node">
+<title>CALL_alignment</title>
+<ellipse fill="none" stroke="black" cx="413.55" cy="-246" rx="60.54" ry="18"/>
+<ellipse fill="none" stroke="black" cx="413.55" cy="-246" rx="64.54" ry="22"/>
+<text text-anchor="middle" x="413.55" y="-240.57" font-family="Times New Roman,serif" font-size="14.00">call alignment</text>
+</g>
+<!-- CALL_alignment&#45;&gt;CALL_mutation_calling -->
+<g id="edge4" class="edge">
+<title>CALL_alignment&#45;&gt;CALL_mutation_calling</title>
+<path fill="none" stroke="black" d="M448.42,-227.11C470.97,-215.53 500.43,-200.42 524.16,-188.24"/>
+<polygon fill="black" stroke="black" points="525.65,-190.9 532.95,-183.22 522.45,-184.67 525.65,-190.9"/>
+</g>
+<!-- CALL_alignment&#45;&gt;CALL_statistics -->
+<g id="edge7" class="edge">
+<title>CALL_alignment&#45;&gt;CALL_statistics</title>
+<path fill="none" stroke="black" d="M357.8,-234.61C301.89,-223.92 213.42,-206.29 137.55,-188 131.5,-186.54 125.2,-184.94 118.93,-183.29"/>
+<polygon fill="black" stroke="black" points="120.02,-179.69 109.45,-180.48 118.21,-186.45 120.02,-179.69"/>
+</g>
+<!-- CALL_alignment&#45;&gt;CALL_fusion -->
+<g id="edge5" class="edge">
+<title>CALL_alignment&#45;&gt;CALL_fusion</title>
+<path fill="none" stroke="black" d="M349.08,-243.31C296.56,-238.99 222.82,-225.9 170.55,-188 146.69,-170.7 130.57,-140.51 121.3,-118.4"/>
+<polygon fill="black" stroke="black" points="124.23,-117.29 117.29,-109.28 117.72,-119.87 124.23,-117.29"/>
+</g>
+<!-- CALL_msi -->
+<g id="node6" class="node">
+<title>CALL_msi</title>
+<ellipse fill="none" stroke="black" cx="308.55" cy="-166" rx="38.59" ry="18"/>
+<text text-anchor="middle" x="308.55" y="-160.57" font-family="Times New Roman,serif" font-size="14.00">call msi</text>
+</g>
+<!-- CALL_alignment&#45;&gt;CALL_msi -->
+<g id="edge3" class="edge">
+<title>CALL_alignment&#45;&gt;CALL_msi</title>
+<path fill="none" stroke="black" d="M387.33,-225.52C372.09,-214.2 352.88,-199.93 337.25,-188.32"/>
+<polygon fill="black" stroke="black" points="339.63,-184.98 329.51,-181.83 335.45,-190.6 339.63,-184.98"/>
+</g>
+<!-- CALL_cnvkit -->
+<g id="node7" class="node">
+<title>CALL_cnvkit</title>
+<ellipse fill="none" stroke="black" cx="413.55" cy="-166" rx="48.07" ry="18"/>
+<text text-anchor="middle" x="413.55" y="-160.57" font-family="Times New Roman,serif" font-size="14.00">call cnvkit</text>
+</g>
+<!-- CALL_alignment&#45;&gt;CALL_cnvkit -->
+<g id="edge6" class="edge">
+<title>CALL_alignment&#45;&gt;CALL_cnvkit</title>
+<path fill="none" stroke="black" d="M413.55,-223.69C413.55,-214.9 413.55,-204.59 413.55,-195.2"/>
+<polygon fill="black" stroke="black" points="417.05,-195.35 413.55,-185.35 410.05,-195.35 417.05,-195.35"/>
+</g>
+<!-- CALL_alignment&#45;&gt;CALL_annovar -->
+<g id="edge12" class="edge">
+<title>CALL_alignment&#45;&gt;CALL_annovar</title>
+<path fill="none" stroke="black" d="M478.25,-244.64C572.99,-242.57 742.38,-232.56 780.55,-188 793.27,-173.15 790.56,-160.8 780.55,-144 770.15,-126.55 751.78,-114.49 733.74,-106.35"/>
+<polygon fill="black" stroke="black" points="735.38,-102.82 724.8,-102.21 732.69,-109.28 735.38,-102.82"/>
+</g>
+<!-- CALL_chemo -->
+<g id="node10" class="node">
+<title>CALL_chemo</title>
+<ellipse fill="none" stroke="black" cx="720.55" cy="-166" rx="50.56" ry="18"/>
+<text text-anchor="middle" x="720.55" y="-160.57" font-family="Times New Roman,serif" font-size="14.00">call chemo</text>
+</g>
+<!-- CALL_alignment&#45;&gt;CALL_chemo -->
+<g id="edge10" class="edge">
+<title>CALL_alignment&#45;&gt;CALL_chemo</title>
+<path fill="none" stroke="black" d="M468.44,-234.14C518.79,-223.75 595.24,-206.9 660.55,-188 665.72,-186.5 671.09,-184.82 676.41,-183.06"/>
+<polygon fill="black" stroke="black" points="677.14,-186.17 685.49,-179.65 674.9,-179.54 677.14,-186.17"/>
+</g>
+<!-- CALL_qc -->
+<g id="node8" class="node">
+<title>CALL_qc</title>
+<ellipse fill="none" stroke="black" cx="413.55" cy="-326" rx="35.1" ry="18"/>
+<ellipse fill="none" stroke="black" cx="413.55" cy="-326" rx="39.1" ry="22"/>
+<text text-anchor="middle" x="413.55" y="-320.57" font-family="Times New Roman,serif" font-size="14.00">call qc</text>
+</g>
+<!-- CALL_qc&#45;&gt;CALL_alignment -->
+<g id="edge8" class="edge">
+<title>CALL_qc&#45;&gt;CALL_alignment</title>
+<path fill="none" stroke="black" d="M413.55,-303.69C413.55,-296.12 413.55,-287.43 413.55,-279.16"/>
+<polygon fill="black" stroke="black" points="417.05,-279.29 413.55,-269.29 410.05,-279.29 417.05,-279.29"/>
+</g>
+<!-- CALL_tmb -->
+<g id="node12" class="node">
+<title>CALL_tmb</title>
+<ellipse fill="none" stroke="black" cx="682.55" cy="-18" rx="40.09" ry="18"/>
+<text text-anchor="middle" x="682.55" y="-12.57" font-family="Times New Roman,serif" font-size="14.00">call tmb</text>
+</g>
+<!-- CALL_annovar&#45;&gt;CALL_tmb -->
+<g id="edge13" class="edge">
+<title>CALL_annovar&#45;&gt;CALL_tmb</title>
+<path fill="none" stroke="black" d="M682.55,-71.7C682.55,-64.24 682.55,-55.32 682.55,-46.97"/>
+<polygon fill="black" stroke="black" points="686.05,-47.1 682.55,-37.1 679.05,-47.1 686.05,-47.1"/>
+</g>
+<!-- CALL_hla -->
+<g id="node11" class="node">
+<title>CALL_hla</title>
+<ellipse fill="none" stroke="black" cx="215.55" cy="-166" rx="36.09" ry="18"/>
+<text text-anchor="middle" x="215.55" y="-160.57" font-family="Times New Roman,serif" font-size="14.00">call hla</text>
+</g>
+<!-- CALL_hla&#45;&gt;CALL_neoantigen -->
+<g id="edge11" class="edge">
+<title>CALL_hla&#45;&gt;CALL_neoantigen</title>
+<path fill="none" stroke="black" d="M224.4,-148.21C229.12,-139.25 235.04,-128.02 240.38,-117.88"/>
+<polygon fill="black" stroke="black" points="243.9,-119.72 245.47,-109.24 237.71,-116.45 243.9,-119.72"/>
+</g>
+<!-- CALL_create_dir -->
+<g id="node13" class="node">
+<title>CALL_create_dir</title>
+<ellipse fill="none" stroke="black" cx="533.55" cy="-326" rx="62.54" ry="18"/>
+<text text-anchor="middle" x="533.55" y="-320.57" font-family="Times New Roman,serif" font-size="14.00">call create_dir</text>
+</g>
+</g>
+</svg>
diff --git a/other/pipeline.dot b/other/pipeline.dot
index 3deeeac..780d398 100644
--- a/other/pipeline.dot
+++ b/other/pipeline.dot
@@ -3,23 +3,23 @@ digraph pipeline {
   compound=true;
 
   # Links
+  CALL_mutation_calling -> CALL_neoantigen
+  CALL_statistics -> CALL_fusion
   CALL_alignment -> CALL_msi
   CALL_alignment -> CALL_mutation_calling
-  CALL_tumor_content -> CALL_cnvkit
   CALL_alignment -> CALL_fusion
   CALL_alignment -> CALL_cnvkit
+  CALL_alignment -> CALL_statistics
   CALL_qc -> CALL_alignment
   CALL_mutation_calling -> CALL_annovar
   CALL_alignment -> CALL_chemo
-  CALL_mutation_calling -> CALL_neoantigen
-  CALL_alignment -> CALL_tumor_content
   CALL_hla -> CALL_neoantigen
   CALL_alignment -> CALL_annovar
   CALL_annovar -> CALL_tmb
 
   # Nodes
   CALL_alignment [label="call alignment";shape="oval";peripheries=2]
-  CALL_tumor_content [label="call tumor_content"]
+  CALL_statistics [label="call statistics";shape="oval";peripheries=2]
   CALL_mutation_calling [label="call mutation_calling"]
   CALL_annovar [label="call annovar"]
   CALL_cnvkit [label="call cnvkit"]