First commit.

.gitignore

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+*.log
+*.DS_Store

README.md

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+## Arguments
+
+```text
+# User Defined
+read1: oss://pgx-storage-results/demo/Quartet-RNA-D5-3-test.clipped_R1.fastq.gz
+read2: oss://pgx-storage-results/demo/Quartet-RNA-D5-3-test.clipped_R2.fastq.gz
+baseout: Quartet-RNA-D5-3-test.clipped
+idx_prefix: genome
+genome_directory: oss://pgx-storage-results/yangjingcheng/reference/genome/
+gtf: oss://pgx-storage-results/yangjingcheng/reference/genome/genes.gtf
+adapter: oss://pgx-storage-results/yangjingcheng/reference/illumina_adapter/TruSeq3-PE.fa
+
+# Default Value
+fastqc_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5
+trimmomatic_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trimmomatic:v0.3.8
+tophat2_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/tophat2:2.0.14
+cuffdiff2_docker: registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cufflinks:v2.2.1
+```

defaults

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+{
+  "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
+  "trimmomatic_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trimmomatic:v0.3.8",
+  "tophat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/tophat2:2.0.14",
+  "cuffdiff2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cufflinks:v2.2.1"
+}

inputs

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+{
+    "{{ project_name }}.read1": "{{ read1 }}",
+    "{{ project_name }}.read2": "{{ read2 }}",
+    "{{ project_name }}.adapter": "{{ adapter }}",
+    "{{ project_name }}.gtf": "{{ gtf }}",
+    "{{ project_name }}.genome_directory": "{{ genome_directory }}",
+    "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
+    "{{ project_name }}.baseout": "{{ baseout }}",
+    "{{ project_name }}.fastqc.docker": "{{ fastqc_docker }}",
+    "{{ project_name }}.trimmomatic.docker": "{{ trimmomatic_docker }}",
+    "{{ project_name }}.tophat2.docker": "{{ tophat2_docker }}",
+    "{{ project_name }}.cuffdiff2.docker": "{{ cuffdiff2_docker }}"
+}

tasks/cuffdiff2.wdl

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+task cuffdiff2 {
+    File bam
+    File gtf
+    File genome_directory
+    String idx_prefix
+    String baseout
+    String docker
+
+    command {
+      cuffdiff ${gtf} -p 24 -o ${baseout} --no-diff -u -L ${baseout},${baseout}_rep -b ${genome_directory}/${idx_prefix}.fa ${bam} ${bam} 
+    }
+
+    runtime {
+      dockerTag: docker
+    }
+    
+    output {
+      File isoforms_count = "${baseout}/isoforms.count_tracking"
+      File genes_count = "${baseout}/genes.count_tracking"
+      File cds_count = "${baseout}/cds.count_tracking"
+      File isoforms_fpkm = "${baseout}/isoforms.fpkm_tracking"
+      File genes_fpkm = "${baseout}/genes.fpkm_tracking"
+      File cds_fpkm = "${baseout}/cds.fpkm_tracking"
+    }
+}

tasks/fastqc.wdl

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+task qc {
+	File read
+	String docker
+	String out_dir = "./"
+
+	command {
+		fastqc -o ${out_dir} ${read}
+	}
+
+	runtime {
+		dockerTag: docker
+	}
+
+	# 输入文件后缀必须为.fq.gz或者.fastq.gz
+	output {
+		File html = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
+		File zip = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
+	}
+}

tasks/tophat2.wdl

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+task tophat2 {
+   File gtf
+   File genome_directory
+   String idx_prefix
+   File read_1P
+   File read_2P
+   String baseout
+   String docker
+
+   command {
+      tophat2 -p 24 -o ${baseout} -G ${gtf} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read_1P} ${read_2P}
+   }
+   
+   runtime { 
+      dockerTag: docker 
+   }
+
+   output {
+      File accepted_hits = "${baseout}/accepted_hits.bam"
+      File unmapped_bam = "${baseout}/unmapped.bam"
+   }
+}

tasks/trimmomatic.wdl

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+task trimmomatic {
+	File read1
+	File read2
+	File adapter
+	String baseout
+	String baseout_gz = baseout + ".fq.gz"
+	String docker
+
+	command {
+  	trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  -baseout ${baseout_gz} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
+	}
+
+	runtime {
+		dockerTag: docker
+	}
+
+	output {
+		File read_1p = baseout + "_1P.fq.gz"
+		File read_2p = baseout + "_2P.fq.gz"
+	}
+}

workflow.wdl

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+import "./tasks/fastqc.wdl" as fastqc
+import "./tasks/trimmomatic.wdl" as trimmomatic
+import "./tasks/tophat2.wdl" as tophat2
+import "./tasks/cuffdiff2.wdl" as cuffdiff2
+
+workflow {{ project_name }} {
+	File read1
+	File read2
+	File adapter
+	String baseout
+
+	File gtf
+	File genome_directory
+	String idx_prefix
+	
+	scatter ( read in [read1, read2]) {
+		call fastqc.qc as fastqc {input: read=read}
+	}
+	
+	call trimmomatic.trimmomatic as trimmomatic {
+		input: baseout=baseout, read1=read1, read2=read2, adapter=adapter
+	}
+
+	call tophat2.tophat2 as tophat2 {
+		input: baseout=baseout, read_1P=trimmomatic.read_1p, read_2P=trimmomatic.read_2p, gtf=gtf, genome_directory=genome_directory, idx_prefix=idx_prefix
+	}
+
+	call cuffdiff2.cuffdiff2 as cuffdiff2 {
+		input: gtf = gtf, bam = tophat2.accepted_hits, genome_directory=genome_directory, idx_prefix=idx_prefix, baseout=baseout
+	}
+        
+	output {
+		Array[File] fastqc_html = fastqc.html
+		Array[File] fastqc_zip = fastqc.zip
+                File fastq_1p = trimmomatic.read_1p
+		File fastq_2p = trimmomatic.read_2p
+                File bam = tophat2.accepted_hits
+		File unmapped_bam = tophat2.unmapped_bam
+                File isoforms_count = cuffdiff2.isoforms_count
+		File genes_count = cuffdiff2.genes_count
+		File cds_count = cuffdiff2.cds_count
+		File isoforms_fpkm = cuffdiff2.isoforms_fpkm
+		File genes_fpkm = cuffdiff2.genes_fpkm
+		File cds_fpkm = cuffdiff2.cds_fpkm
+	}
+}
+
+