first commit

inputs

+{
+    "{{ project_name }}.read1": "{{ read1 }}",
+    "{{ project_name }}.read2": "{{ read2 }}",
+    "{{ project_name }}.idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
+    "{{ project_name }}.gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
+    "{{ project_name }}.idx_prefix": "genome_snp_tran",
+    "{{ project_name }}.hisat2.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.0.5-1-deb-cv1",
+    "{{ project_name }}.hisat2.cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+    "{{ project_name }}.samtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+    "{{ project_name }}.samtools.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "{{ project_name }}.stringtie.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
+    "{{ project_name }}.stringtie.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
+}

tasks/fastqc.wdl

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

tasks/hisat2.wdl

+task hisat2 {
+   File idx
+   File read_1P
+   File read_2P
+   String idx_prefix
+   String base = sub(basename(read_1P),"\\.\\S+$", "")
+   String docker
+   String cluster
+
+   command {
+   	 nt=$(nproc)
+     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam
+   }
+   
+   runtime { 
+		docker: docker 
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd 200 /cromwell_root/"
+   }
+
+   output {
+      File sam = base + ".sam"
+   }
+}

tasks/samtools.wdl

+task samtools {
+    File sam
+    String base = basename(sam, ".sam")
+    String bam = base + ".bam"
+    String sorted_bam = base + ".sorted.bam"
+    String sorted_bam_index = base + ".sorted.bam.bai"
+    String docker
+    String cluster
+
+    command <<<
+       set -o pipefail
+       set -e
+       /opt/conda/bin/samtools view -bS ${sam} > ${bam}
+       /opt/conda/bin/samtools sort -m 5000000000 ${bam} -o ${sorted_bam}
+       /opt/conda/bin/samtools index ${sorted_bam}
+    >>>
+
+    runtime {
+       docker: docker
+       cluster: cluster
+       systemDisk: "cloud_ssd 40"
+       dataDisk: "cloud_ssd 200 /cromwell_root/"
+    }
+
+    output {
+      File out_bam = sorted_bam
+      File out_bam_index = sorted_bam_index
+    }
+
+}
+

tasks/stringtie.wdl

+task stringtie {
+    File bam
+    File gtf
+    String docker
+    String base = basename(bam, ".sorted.bam")
+    String cluster
+
+    command <<<
+      nt=$(nproc)
+      mkdir ballgown
+      /opt/conda/bin/stringtie -e -B -p $nt -G ${gtf} -o ballgown/${base}/${base}.gtf -C ${base}.cov.ref.gtf -A ${base}.gene.abundance.txt ${bam}
+    >>>
+    
+    runtime {
+      docker: docker
+      cluster: cluster
+      systemDisk: "cloud_ssd 40"
+      dataDisk: "cloud_ssd 150 /cromwell_root/"
+    }
+    
+    output {
+      File covered_transcripts = "${base}.cov.ref.gtf"
+      File gene_abundance = "${base}.gene.abundance.txt"
+      Array[File] ballgown = ["ballgown/${base}/${base}.gtf", "ballgown/${base}/e2t.ctab", "ballgown/${base}/e_data.ctab", "ballgown/${base}/i2t.ctab", "ballgown/${base}/i_data.ctab", "ballgown/${base}/t_data.ctab"]
+    }
+}

tasks/trimmomatic.wdl

+task trimmomatic {
+	File read1
+	File read2
+	File adapter
+	String baseout
+        String baseout_gz = baseout + ".fq.gz"
+	String docker
+	String cluster
+
+	command {
+           /opt/conda/bin/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 {
+	   docker: docker
+	   cluster: cluster
+	}
+
+        output {
+           File read_1p = baseout + "_1P.fq.gz"
+           File read_2p = baseout + "_2P.fq.gz"
+	}
+}

workflow.wdl

+import "./tasks/hisat2.wdl" as hisat2
+import "./tasks/samtools.wdl" as samtools
+import "./tasks/stringtie.wdl" as stringtie
+
+workflow {{ project_name }} {
+
+	File read1
+	File read2
+        File idx
+	String idx_prefix
+        File gtf
+	
+	
+	call hisat2.hisat2 as hisat2 {
+		input: idx=idx, idx_prefix=idx_prefix, read_1P=read1, read_2P=read2
+	}
+
+        call samtools.samtools as samtools {
+               input: sam = hisat2.sam
+	}
+
+        call stringtie.stringtie as stringtie {
+              input: gtf = gtf, bam = samtools.out_bam
+	}
+        
+	
+}
+
+