first commit

inputs

+{
+  "{{ project_name }}.idx_prefix": "genome_snp_tran",
+  "{{ project_name }}.stringtie.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
+  "{{ project_name }}.samtools.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "{{ project_name }}.samtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+  "{{ project_name }}.idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
+  "{{ project_name }}.read2": "{{ read2 }}",
+  "{{ project_name }}.read1": "{{ read1 }}",
+  "{{ project_name }}.anno_gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.stringtie.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "{{ project_name }}.hisat2.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",
+  "{{ project_name }}.hisat2.cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"
+}

tasks/hisat2.wdl

+task hisat2 {
+   File idx
+   File read1
+   File read2
+   String idx_prefix
+   String sample_id
+   String docker
+   String cluster
+
+   command {
+   	 nt=$(nproc)
+
+       hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read1} -2 ${read2} -S ${sample_id}.sam --novel-splicesite-outfile ${sample_id}.splicesite.tab --dta
+
+   }
+   
+   runtime { 
+		docker: docker 
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd 200 /cromwell_root/"
+   }
+
+   output {
+      File sam = "${sample_id}.sam"
+      File splicesite = "${sample_id}.splicesite.tab"
+   }
+}

tasks/samtools.wdl

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

tasks/stringtie.wdl

+task stringtie {
+    File bam
+    File anno_gtf
+    String docker
+    String sample_id
+    String cluster
+
+    command <<<
+      nt=$(nproc)
+      /opt/conda/bin/stringtie -p $nt -G ${anno_gtf} -o ${sample_id}.gtf -l CUFF ${bam}
+    >>>
+    
+    runtime {
+      docker: docker
+      cluster: cluster
+      systemDisk: "cloud_ssd 40"
+      dataDisk: "cloud_ssd 150 /cromwell_root/"
+    }
+    
+    output {
+      File gtf = "${sample_id}.gtf"
+    }
+}

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 anno_gtf
+	String sample_id
+	
+	
+	call hisat2.hisat2 as hisat2 {
+		input: 
+		idx=idx, 
+		idx_prefix=idx_prefix, 
+		read1=read1,
+		read2=read2,
+		sample_id=sample_id
+	}
+
+    call samtools.samtools as samtools {
+        input: 
+		sample_id=sample_id, 
+		sam = hisat2.sam
+	}
+
+    call stringtie.stringtie as stringtie {
+        input: 
+		anno_gtf = anno_gtf, 
+		bam = samtools.out_bam,
+		sample_id=sample_id
+	}
+       	
+}
+