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README.md

 | --------- | --------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------- | ----------- | ------------ |
 | FDU_D5    | 200       | oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R1_400k.gz | oss://choppy-app-example-data/RNAseq/Downsampling_Quartet_RNAseqQC_12samples/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_D5_1_20190710_CleanData_R2_400k.gz | false            | true        | true         |
 
+
 - sample_id： 一般设置为文件输出前缀
 - read1： R1 fastq 文件所在路径
 - read2： R2 fastq 文件所在路径

defaults

 {
-    "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
-    "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
-    "idx_prefix": "genome_snp_tran",
-    "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
-    "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
-    "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
-    "fastqscreen_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
-    "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
-    "fastqc_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
-    "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
-    "fastp_cluster": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
-    "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
-    "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
-    "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",
-    "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
-    "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
-    "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
-    "qualimap_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
-    "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
-    "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",
-    "ballgown_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
-    "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/count:v1.0",
-    "count_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
-    "insert_size":"8000",
-    "count_length": "150"
+  "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
+  "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
+  "idx_prefix": "genome_snp_tran",
+  "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
+  "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
+  "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
+  "fastqscreen_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
+  "fastqc_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
+  "fastp_cluster": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
+  "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
+  "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
+  "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",
+  "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+  "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+  "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+  "qualimap_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+  "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
+  "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",
+  "ballgown_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
+  "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/count:v1.0",
+  "count_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
+  "insert_size":"8000",
+  "count_length": "150",
+  "trim_adapter": true,
+  "pre_alignment_qc": true,
+  "qualimap_qc": true
 }

inputs

 {
-    "{{ project_name }}.read1": "{{ read1 }}",
-    "{{ project_name }}.read2": "{{ read2 }}",
-    "{{ project_name }}.sample_id": "{{ sample_id }}",
-    "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
-    "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
-    "{{ project_name }}.idx": "{{ idx }}",
-    "{{ project_name }}.gtf": "{{ gtf }}",
-    "{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}",
-    "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
-    "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
-    "{{ project_name }}.fastqscreen_cluster": "{{ fastqscreen_cluster }}",
-    "{{ project_name }}.fastqc_cluster": "{{ fastqc_cluster }}",
-    "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
-    "{{ project_name }}.fastp_docker": "{{ fastp_docker }}",
-    "{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}",
-    "{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}",
-    "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
-    "{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}",
-    "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
-    "{{ project_name }}.insert_size": "{{ insert_size }}",
-    "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
-    "{{ project_name }}.samtools_cluster": "{{ samtools_cluster }}",
-    "{{ project_name }}.qualimap_docker": "{{ qualimap_docker }}",
-    "{{ project_name }}.qualimap_cluster": "{{ qualimap_cluster }}",
-    "{{ project_name }}.stringtie_docker": "{{ stringtie_docker }}",
-    "{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster }}",
-    "{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
-    "{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}",
-    "{{ project_name }}.count_docker": "{{ count_docker }}",
-    "{{ project_name }}.count_cluster": "{{ count_cluster }}",
-    "{{ project_name }}.count_length": "{{ count_length }}",
-    "{{ project_name }}.trim_adapter":  true,
-    "{{ project_name }}.pre_alignment_qc": true,
-    "{{ project_name }}.qualimap_qc": true
+  "{{ project_name }}.read1": "{{ read1 }}",
+  "{{ project_name }}.read2": "{{ read2 }}",
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
+  "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
+  "{{ project_name }}.idx": "{{ idx }}",
+  "{{ project_name }}.gtf": "{{ gtf }}",
+  "{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}",
+  "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
+  "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
+  "{{ project_name }}.fastqscreen_cluster": "{{ fastqscreen_cluster }}",
+  "{{ project_name }}.fastqc_cluster": "{{ fastqc_cluster }}",
+  "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
+  "{{ project_name }}.fastp_docker": "{{ fastp_docker }}",
+  "{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}",
+  "{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}",
+  "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
+  "{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}",
+  "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
+  "{{ project_name }}.insert_size": "{{ insert_size }}",
+  "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
+  "{{ project_name }}.samtools_cluster": "{{ samtools_cluster }}",
+  "{{ project_name }}.qualimap_docker": "{{ qualimap_docker }}",
+  "{{ project_name }}.qualimap_cluster": "{{ qualimap_cluster }}",
+  "{{ project_name }}.stringtie_docker": "{{ stringtie_docker }}",
+  "{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster }}",
+  "{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
+  "{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}",
+  "{{ project_name }}.count_docker": "{{ count_docker }}",
+  "{{ project_name }}.count_cluster": "{{ count_cluster }}",
+  "{{ project_name }}.count_length": "{{ count_length }}",
+  "{{ project_name }}.trim_adapter":  {{ trim_adapter }},
+  "{{ project_name }}.pre_alignment_qc": {{ pre_alignment_qc }},
+  "{{ project_name }}.qualimap_qc": {{ qualimap_qc }}
 }

tasks/ballgown.wdl

 task ballgown {
-    File gene_abundance
-    String base=basename(gene_abundance, ".gene.abundance.txt")
-    String docker
-    String cluster
-    String disk_size
-    Array[File] ballgown
+  File gene_abundance
+  String base=basename(gene_abundance, ".gene.abundance.txt")
+  String docker
+  String cluster
+  String disk_size
+  Array[File] ballgown
 
-    command <<<
-      mkdir -p /cromwell_root/tmp/${base}
-      cp -r ${sep=" " ballgown} /cromwell_root/tmp/${base}
-      ballgown /cromwell_root/tmp/${base} ${base}.txt
-      sed -i 's/"//g' ${base}.txt
-      sed -i '1s/FPKM./GENE_ID\t/g' ${base}.txt
-    >>>
-    
-    runtime {
-      docker: docker
-      cluster: cluster
-      systemDisk: "cloud_ssd 40"
-      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    
-    output {
-      File mat_expression="${base}.txt"
-    }
+  command <<<
+    mkdir -p /cromwell_root/tmp/${base}
+    cp -r ${sep=" " ballgown} /cromwell_root/tmp/${base}
+    ballgown /cromwell_root/tmp/${base} ${base}.txt
+    sed -i 's/"//g' ${base}.txt
+    sed -i '1s/FPKM./GENE_ID\t/g' ${base}.txt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File mat_expression="${base}.txt"
+  }
 }

tasks/count.wdl

 task count {
-    Array[File] ballgown
-    String sample_id
-    String docker
-    String cluster
-    String disk_size
-    Int count_length
+  Array[File] ballgown
+  String sample_id
+  String docker
+  String cluster
+  String disk_size
+  Int count_length
 
-    command <<<
-      mkdir -p /cromwell_root/tmp/ballgown/${sample_id}
-      cp -r ${sep=" " ballgown} /cromwell_root/tmp/ballgown/${sample_id}
-      count -i /cromwell_root/tmp/ballgown -l ${count_length} -g ${sample_id}_gene_count_matrix.csv -t ${sample_id}_transcript_count_matrix.csv
-    >>>
-    
-    runtime {
-      docker: docker
-      cluster: cluster
-      systemDisk: "cloud_ssd 40"
-      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    
-    output {
-      File mat_expression_genecount="${sample_id}_gene_count_matrix.csv"
-      File mat_expression_transcriptcount="${sample_id}_transcript_count_matrix.csv"
-    }
+  command <<<
+    mkdir -p /cromwell_root/tmp/ballgown/${sample_id}
+    cp -r ${sep=" " ballgown} /cromwell_root/tmp/ballgown/${sample_id}
+    count -i /cromwell_root/tmp/ballgown -l ${count_length} -g ${sample_id}_gene_count_matrix.csv -t ${sample_id}_transcript_count_matrix.csv
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File mat_expression_genecount="${sample_id}_gene_count_matrix.csv"
+    File mat_expression_transcriptcount="${sample_id}_transcript_count_matrix.csv"
+  }
 }

tasks/fastp.wdl

 task fastp {
-    File read1
-    File read2
-    String sample_id
-    String adapter_sequence
-    String adapter_sequence_r2
-    String docker
-    String cluster
-    String disk_size
-    String trim_adapter
+  File read1
+  File read2
+  String sample_id
+  String adapter_sequence
+  String adapter_sequence_r2
+  String docker
+  String cluster
+  String disk_size
+  String trim_adapter
 
-	command <<<
-        nt=$(nproc)
-        
-        ## Trim
-        if [ "${trim_adapter}" != 'true' ]; then
-        cp ${read1} ${sample_id}_R1.fq.gz
-        cp ${read2} ${sample_id}_R2.fq.gz
-        else
-        fastp --thread $nt --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html
-        fi
-   >>>
-   
-   runtime { 
-		docker: docker
-		cluster: cluster
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-   }
+command <<<
+    nt=$(nproc)
+    
+    ## Trim
+    if [ "${trim_adapter}" != 'true' ]; then
+    cp ${read1} ${sample_id}_R1.fq.gz
+    cp ${read2} ${sample_id}_R2.fq.gz
+    else
+    fastp --thread $nt --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe -i ${read1} -I ${read2} -o ${sample_id}_R1.fq.gz -O ${sample_id}_R2.fq.gz -j ${sample_id}.json -h ${sample_id}.html
+    fi
+  >>>
+  
+  runtime { 
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-   output {
-      File json = "${sample_id}.json"
-      File report = "${sample_id}.html"
-      File trim_R1 = "${sample_id}_R1.fq.gz"
-      File trim_R2 = "${sample_id}_R2.fq.gz"
-   }
+  output {
+    File json = "${sample_id}.json"
+    File report = "${sample_id}.html"
+    File trim_R1 = "${sample_id}_R1.fq.gz"
+    File trim_R2 = "${sample_id}_R2.fq.gz"
+  }
 }

tasks/hisat2.wdl

 task hisat2 {
-   File idx
-   File read_1P
-   File read_2P
-   String idx_prefix
-   String sample_id
-   String docker
-   String cluster
-   String disk_size
+  File idx
+  File read_1P
+  File read_2P
+  String idx_prefix
+  String sample_id
+  String docker
+  String cluster
+  String disk_size
    
 
-   command {
-      nt=$(nproc)
-      hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${sample_id}.sam  --un-conc-gz ${sample_id}_un.fq.gz
-   }
+  command {
+    nt=$(nproc)
+    hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${sample_id}.sam  --un-conc-gz ${sample_id}_un.fq.gz
+  }
    
-   runtime { 
-      docker: docker
-      cluster: cluster
-      systemDisk: "cloud_ssd 40"
-      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-   }
+  runtime { 
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /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"
-   }
+  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/qualimap.wdl

 		nt=$(nproc)
 		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
 		tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc
-		
 	>>>
 
 	runtime {
-		docker:docker
-		cluster:cluster
-		systemDisk:"cloud_ssd 40"
-		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+		docker: docker
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 
 	output {

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 samstats=base + ".samstats"
-    String ins_size=base + ".ins_size"
-    String docker
-    String cluster
-    String disk_size
-    Int insert_size
+  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 samstats=base + ".samstats"
+  String ins_size=base + ".ins_size"
+  String docker
+  String cluster
+  String disk_size
+  Int insert_size
 
-    command <<<
-       set -o pipefail
-       set -e
-       nt=$(nproc)
-       /opt/conda/bin/samtools view -@ $nt -bS ${sam} > ${bam}
-       /opt/conda/bin/samtools sort -@ $nt -m 1000000000 ${bam} -o ${sorted_bam}
-       /opt/conda/bin/samtools index ${sorted_bam}
-       /opt/conda/bin/samtools stats ${sorted_bam} > ${samstats}
-       /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size}
-    >>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    /opt/conda/bin/samtools view -@ $nt -bS ${sam} > ${bam}
+    /opt/conda/bin/samtools sort -@ $nt -m 1000000000 ${bam} -o ${sorted_bam}
+    /opt/conda/bin/samtools index ${sorted_bam}
+    /opt/conda/bin/samtools stats ${sorted_bam} > ${samstats}
+    /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size}
+  >>>
 
-    runtime {
-       docker: docker
-       cluster: cluster
-       systemDisk: "cloud_ssd 40"
-       dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
+  runtime {
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-    output {
-       File out_sort_bam="${sorted_bam}"
-       File out_sort_bam_index="${sorted_bam_index}"
-       File out_samstats="${samstats}"
-       File out_ins_size="${ins_size}"
-    }
+  output {
+    File out_sort_bam="${sorted_bam}"
+    File out_sort_bam_index="${sorted_bam_index}"
+    File out_samstats="${samstats}"
+    File out_ins_size="${ins_size}"
+  }
 
 }
 

tasks/stringtie.wdl

 task stringtie {
-    File bam
-    File gtf
-    String docker
-    String base=basename(bam, ".sorted.bam")
-    String cluster
-    String disk_size
+  File bam
+  File gtf
+  String docker
+  String base=basename(bam, ".sorted.bam")
+  String cluster
+  String disk_size
 
-    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 ${bam}
-    >>>
-    
-    runtime {
-      docker: docker
-      cluster: cluster
-      systemDisk: "cloud_ssd 40"
-      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    
-    output {
-      File covered_transcripts="${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"]
-    }
+  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 ${bam}
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File covered_transcripts="${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"]
+  }
 }

workflow.wdl

 import "./tasks/count.wdl" as count
 
 workflow {{ project_name }} {
-	
 	File read1
 	File read2
 	File idx
 			docker=fastqc_docker,
 			cluster=fastqc_cluster,
 			disk_size=disk_size
-			}
+		}
 		
 		call fastqscreen.fastqscreen as fastqscreen {
 			input:
 			screen_ref_dir=screen_ref_dir,
 			fastq_screen_conf=fastq_screen_conf,
 			disk_size=disk_size
-			}	
-			}
+		}	
+	}
 
 	call fastp.fastp as fastp {
 		input:
 		adapter_sequence=adapter_sequence,
 		adapter_sequence_r2=adapter_sequence_r2,
 		trim_adapter=trim_adapter
-		}
+	}
 			
 	call hisat2.hisat2 as hisat2 {
 		input:
 		read_1P=fastp.trim_R1,
 		read_2P=fastp.trim_R2,
 		disk_size=disk_size
-		}
+	}
 	
 	call samtools.samtools as samtools {
 		input:
 		sam=hisat2.sam,
 		insert_size=insert_size,
 		disk_size=disk_size
-		}
+	}
 
 	if (qualimap_qc){
 		call qualimap.qualimap as qualimap {
 			docker=qualimap_docker,
 			cluster=qualimap_cluster,
 			disk_size=disk_size
-			}
-			}
+		}
+	}
 
 	call stringtie.stringtie as stringtie {
 		input:
 		gtf=gtf,
 		bam=samtools.out_sort_bam,
 		disk_size=disk_size
-		}
+	}
 
 	call ballgown.ballgown as ballgown {
 		input:
 		ballgown=stringtie.ballgown,
 		gene_abundance=stringtie.gene_abundance,
 		disk_size=disk_size
-		}
+	}
 	
 	call count.count as count {
 		input: