first commit

inputs

+{
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ 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",
+    "{{ project_name }}.fastp.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
+    "{{ project_name }}.fastp.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "{{ project_name }}.adapter_sequence": "{{ adapter_sequence if adapter_sequence != '' else 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' }}",
+    "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 if adapter_sequence_r2 != '' else 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT' }}"
+}

tasks/fastp.wdl

+task fastp {
+    String sample_id
+    File read1
+    File read2
+    String adapter_sequence
+    String adapter_sequence_r2
+    String docker
+    String cluster
+
+   command <<<
+     fastp --thread 4 -l 50 -q 20 -u 20 --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i  ${read1} -I ${read2} -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
+   >>>
+   
+   runtime { 
+		docker: docker 
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd 200 /cromwell_root/"
+   }
+
+   output {
+      File json = "${sample_id}.json"
+      File report = "${sample_id}.html"
+      File Trim_R1 = "${sample_id}_R1.fastq.gz"
+      File Trim_R2 = "${sample_id}_R2.fastq.gz"
+   }
+}
+
+
+

tasks/hisat2.wdl

+task hisat2 {
+   File idx
+   File Trim_R1
+   File Trim_R2
+   String idx_prefix
+   String sample_id
+   String docker
+   String cluster
+
+   command <<<
+   	 nt=$(nproc)
+     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${Trim_R1} -2 ${Trim_R2} -S ${sample_id}.sam  --un-conc-gz ${sample_id}_un.fq.gz
+   >>>
+   
+   runtime { 
+		docker: docker 
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd 200 /cromwell_root/"
+   }
+
+   output {
+      File sam = "${sample_id}.sam"
+      File unmapread_1p = "${sample_id}_un.fq.1.gz"
+      File unmapread_2p = "${sample_id}_un.fq.2.gz"
+   }
+}

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 ins_size = sample_id + ".ins_size"
+    String docker
+    String cluster
+
+    command <<<
+       set -o pipefail
+       set -e
+       /opt/conda/bin/samtools view -bS ${sam} > ${bam}
+       /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
+       /opt/conda/bin/samtools index ${sorted_bam}
+       /opt/conda/bin/samtools stats -i 8000 ${sorted_bam} |grep ^IS|cut -f 2- > ${sample_id}.ins_size
+    >>>
+
+    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
+      File out_ins_size = ins_size
+    }
+
+}
+

tasks/stringtie.wdl

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

workflow.wdl

+import "./tasks/fastp.wdl" as fastp
+import "./tasks/hisat2.wdl" as hisat2
+import "./tasks/samtools.wdl" as samtools
+import "./tasks/stringtie.wdl" as stringtie
+
+workflow {{ project_name }} {
+
+	String sample_id
+	File read1
+	File read2
+        File idx
+	String adapter_sequence
+        String adapter_sequence_r2
+	String idx_prefix
+        File gtf
+	
+	call fastp.fastp as fastp {
+        input:
+		sample_id=sample_id, 
+		read1=read1, 
+		read2=read2, 
+		adapter_sequence=adapter_sequence, 
+		adapter_sequence_r2=adapter_sequence_r2
+    }
+	
+	call hisat2.hisat2 as hisat2 {
+	input: 
+		sample_id=sample_id, 
+		idx=idx, 
+		idx_prefix=idx_prefix, 
+		Trim_R1=fastp.Trim_R1, 
+		Trim_R2=fastp.Trim_R2
+	}
+
+        call samtools.samtools as samtools {
+               input: 
+		sample_id=sample_id, 
+		sam = hisat2.sam 
+	}
+
+        call stringtie.stringtie as stringtie {
+              input: 
+		gtf = gtf, 
+		bam = samtools.out_bam ,
+		sample_id=sample_id
+	}
+}
+
+