sentieon quality yeild

codescript/.gitignore

@@ -0,0 +1,89 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject

codescript/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2016 Shifu Chen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

codescript/README.md

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+# q30
+A simple script to calculate q20/q30 percentages of a fastq file (can be gzipped)
+```shell
+python q30.py <fastq_file_name>
+```
+# output
+```
+('total bases:', 1386659)
+('q20 bases:', 1280980)
+('q30 bases:', 1232024)
+('q20 percents:', 92.37887613320939)
+('q30 percents:', 88.84837584438567)
+Time used: 0.221389055252
+```

codescript/fastq.py

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+ #!/usr/bin/env python
+  
+import gzip
+import os,sys
+
+def isFastq(f):
+    fqext = (".fq", ".fastq", "fq.gz", ".fastq.gz")
+    for ext in fqext:
+        if f.endswith(ext):
+            return True
+    return False
+
+################################
+#fastq.reader
+
+class Reader:
+
+    def __init__(self, fname):
+        self.__file = None
+        self.__gz = False
+        self.__eof = False
+        self.filename = fname
+        if self.filename.endswith(".gz"):
+            self.__gz = True
+            self.__file = gzip.open(self.filename, "r")
+        else:
+            self.__gz = False
+            self.__file = open(self.filename, "r")
+        if self.__file == None:
+            print("Failed to open file " + self.filename)
+            sys.exit(1)
+            
+    def __del__(self):
+        if self.__file != None:
+            self.__file.close()
+            
+    def nextRead(self):
+        if self.__eof == True or self.__file == None:
+            return None
+
+        lines = []
+        #read 4 (lines, name, sequence, strand, quality)
+        for i in range(0,4):
+            line = self.__file.readline().rstrip()
+            if len(line) == 0:
+                self.__eof = True
+                return None
+            lines.append(line)
+        return lines
+
+    def isEOF(self):
+        return False
+
+################################
+#fastq.writer
+
+class Writer:
+    
+    filename = ""
+    
+    __file = None
+    __gz = False
+    
+    def __init__(self, fname):
+        self.filename = fname
+        if self.filename.endswith(".gz"):
+            self.__gz = True
+            self.__file = gzip.open(self.filename, "w")
+        else:
+            self.__gz = False
+            self.__file = open(self.filename, "w")
+        if self.__file == None:
+            print("Failed to open file " + self.filename + " to write")
+            sys.exit(1)
+            
+    def __del__(self):
+        if self.__file != None:
+            self.__file.flush()
+            self.__file.close()
+
+    def flush(self):
+        if self.__file !=None:
+            self.__file.flush()
+ 
+    def writeLines(self, lines):
+        if self.__file == None:
+            return False
+            
+        for line in lines:
+            self.__file.write(line+"\n")
+        return True
+            
+    def writeRead(self, name, seqence, strand, quality):
+        if self.__file == None:
+            return False
+            
+        self.__file.write(name+"\n")
+        self.__file.write(seqence+"\n")
+        self.__file.write(strand+"\n")
+        self.__file.write(quality+"\n")
+        
+        return True

codescript/q30.py

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+#!/usr/bin/env python
+
+import os,sys
+import fastq
+import time
+
+def qual_stat(qstr):
+    q20 = 0
+    q30 = 0
+    for q in qstr:
+        qual = int(q) - 33
+        if qual >= 30:
+            q30 += 1
+            q20 += 1
+        elif qual >= 20:
+            q20 += 1
+    return q20, q30
+
+def stat(filename):
+    reader = fastq.Reader(filename)
+    total_count = 0
+    q20_count = 0
+    q30_count = 0
+    while True:
+        read = reader.nextRead()
+        if read == None:
+            break
+        total_count += len(read[3])
+        q20, q30 = qual_stat(read[3])
+        q20_count += q20
+        q30_count += q30
+
+    print("total bases:", total_count)
+    print("q20 bases:", q20_count)
+    print("q30 bases:", q30_count)
+    print("q20 percents:", 100 * float(q20_count)/float(total_count))
+    print("q30 percents:", 100 * float(q30_count)/float(total_count))
+
+def main():
+    if len(sys.argv) < 2:
+        print("usage: python q30.py <fastq_file>")
+        sys.exit(1)
+    stat(sys.argv[1])
+
+if __name__ == "__main__":
+    time1 = time.time()
+    main()
+    time2 = time.time()
+    print('Time used: ' + str(time2-time1))

inputs

@@ -1,7 +1,11 @@
 {
-  "{{ project_name }}.disk_size": "100",
-  "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
-  "{{ project_name }}.fastq": "{{ fastq }}",
-  "{{ project_name }}.cluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
-  "{{ project_name }}.sample": "{{ sample }}"
-}
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "{{ project_name }}.Dedup_bam": "{{ Dedup_bam }}",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.disk_size": "500",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "{{ project_name }}.Dedup_bam_index": "{{ Dedup_bam_index }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+}

tasks/deduped_Metrics.wdl

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+task deduped_Metrics {
+
+    File ref_dir
+    
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String fasta
+	File Dedup_bam
+	File Dedup_bam_index
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo QualityYield ${sample}_deduped_QualityYield
+
+		ls > file
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
+	}
+
+	output {
+		File deduped_QualityYield = "${sample}_deduped_QualityYield"
+		File files = "file"
+	}
+}

tasks/q30.wdl

@@ -1,22 +0,0 @@
-task q30 {
-	File fastq
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-	
-	command <<<
-		python /opt/q30.py ${fastq} > ${sample}.q30.txt
-
-	>>>
-
-	runtime {
-		docker:docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File result = "${sample}.q30.txt"
-	}
-}

workflow.wdl

@@ -1,16 +1,24 @@
-import "./tasks/q30.wdl" as q30
+import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
 
 workflow {{ project_name }} {
-	File fastq
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
 	String sample
+	String fasta
+	File Dedup_bam
+	File Dedup_bam_index
 	String docker
 	String cluster_config
 	String disk_size
 
-	call q30.q30 as q30 {
+	call deduped_Metrics.deduped_Metrics as deduped_Metrics {
 		input:	
-		fastq=fastq,
+		ref_dir=ref_dir,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		sample=sample,
+		fasta=fasta,
+		Dedup_bam=Dedup_bam,
+		Dedup_bam_index=Dedup_bam_index,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size