上传文件至 'tasks'

tasks/Haplotyper.wdl

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+task Haplotyper {
+  
+  File ref_dir
+  String fasta
+  File dbsnp_dir
+  
+  String SENTIEON_LICENSE
+  File recaled_bam
+  File recaled_bam_index
+  String dbsnp
+  String sample
+  String docker
+  String cluster_config
+  String disk_size
+  
+  File? regions
+  Int? interval_padding
+  
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+
+    sentieon driver -t $nt \
+    $INTERVAL -r ${ref_dir}/${fasta} \
+    -i ${recaled_bam} \
+    --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} \
+    ${sample}.Haplotyper.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File vcf = "${sample}.Haplotyper.vcf"
+    File vcf_idx = "${sample}.Haplotyper.vcf.idx"
+  }
+}

tasks/MSIsensor.wdl

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+
+task MSIsensor {
+  
+  String sample
+  File ref_dir
+  String fasta
+  File tumor_bam
+  File tumor_bam_index
+  File? normal_bam
+  File? normal_bam_index
+  File baseline
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    # MSI
+    mkdir -p /cromwell_root/tmp/
+    msisensor-pro scan -d ${ref_dir}/${fasta} -o reference.list
+    if [ ${normal_bam} ]; then
+      msisensor-pro msi -d reference.list -n ${normal_bam} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
+    else
+      msisensor-pro pro -d ${baseline} -t ${tumor_bam} -o /cromwell_root/tmp/${sample}
+    fi
+    cp /cromwell_root/tmp/${sample} ${sample}.MSI.txt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File msi = "${sample}.MSI.txt"
+  }
+}

tasks/fastqTobam.wdl

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+task SentieonFastqToBam {
+    # 工具输入文件和参数
+    File fastq1
+    File fastq2
+    String sample_id
+    String Seq_platform
+    String ref_fasta
+    File ref_fasta_dir
+    String SENTIEON_LICENSE
+
+    String docker
+    String cluster_config
+    String disk_size
+
+    ## Extra driver parameters
+    String qc_driver_args = ""
+    String lc_driver_args = "--traverse_param=200000/10000"
+    String dedup_driver_args = "--traverse_param=200000/10000"
+    ## Extra algo parameters
+    String bwa_args = "-Y -M"
+    String bwa_chunk_size = "100000000"
+    String lc_args = ""
+    String bam_option = "--bam_compression 1"
+
+
+
+    
+    String out_bam = sample_id + ".dedup.bam"
+    String out_bai = sample_id + ".dedup.bam.bai"
+
+    # 工具运行命令
+    command <<<
+        set -exo pipefail
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        nt=$(nproc)
+        
+        sentieon bwa mem -R "@RG\tID:${sample_id}\tSM:${sample_id}\tPL:${Seq_platform}" ${bwa_args} -K ${bwa_chunk_size} -t $nt ${ref_fasta_dir}/${ref_fasta} ${fastq1} ${fastq2} \
+        | sentieon util sort ${bam_option} -i - -r ${ref_fasta_dir}/${ref_fasta} -t $nt -o ${sample_id}.sorted.bam --sam2bam
+
+        ls ./
+                  
+        sentieon driver -r ${ref_fasta_dir}/${ref_fasta} -t $nt -i ${sample_id}.sorted.bam ${qc_driver_args} \
+        --algo MeanQualityByCycle ${sample_id}.mq_metrics.txt \
+        --algo QualDistribution ${sample_id}.qd_metrics.txt \
+        --algo GCBias --summary ${sample_id}.gc_summary_metrics.txt ${sample_id}.gc_metrics.txt \
+        --algo AlignmentStat ${sample_id}.aln_metrics.txt \
+        --algo InsertSizeMetricAlgo ${sample_id}.is_metrics.txt
+                  
+        ls ./
+
+        sentieon driver -r ${ref_fasta_dir}/${ref_fasta} -t $nt -i ${sample_id}.sorted.bam ${lc_driver_args} \
+         --algo LocusCollector \
+         ${lc_args} \
+         ${sample_id}.score.txt.gz
+                  
+        ls ./
+
+        sentieon driver -r ${ref_fasta_dir}/${ref_fasta} -t $nt -i ${sample_id}.sorted.bam ${dedup_driver_args} \
+         --algo Dedup \
+         --score_info ${sample_id}.score.txt.gz \
+         --metrics ${sample_id}.dedup_metrics.txt \
+         ${bam_option} ${out_bam} 
+         ls ./
+
+    >>>
+
+
+    runtime {
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+    }
+    
+
+    # 工具运行输出结果
+    output {
+        File deduped_bam = out_bam
+        File deduped_bam_bai = out_bai
+        Array[File] qc_metrics = glob("*_metrics.txt")
+    }
+
+}

tasks/manta.wdl

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+task manta_calling{
+    File tumor_bam
+    File tumor_bam_bai
+    File normal_bam
+    File normal_bam_bai
+    String ref_fasta
+    File ref_dir
+    String sample_id
+    
+    String docker
+    String cluster_config
+    String disk_size
+
+    
+    String out_dir = "${sample_id}_result"
+    command <<<
+    set -exo pipefail
+    nt=$(nproc)
+    /home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \
+    --normalBam ${normal_bam} \
+    --tumorBam ${tumor_bam} \
+    --referenceFasta ${ref_dir}/${ref_fasta} \
+    --runDir ${out_dir}
+    
+    ls ${out_dir}
+
+    python2.7 ${out_dir}/runWorkflow.py -m local -j $nt
+
+    ls ${out_dir}
+
+    tar cvf ${out_dir}.tar ${out_dir}
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+    }
+
+    output{
+        File out_file = "${out_dir}.tar"
+        File manta_indel_vcf = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz"
+        File manta_indel_vcf_index = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz.tbi"
+    }
+}

tasks/qualimap.wdl

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+task qualimap{
+    String sample_id
+    File bam_file
+    File bam_bai
+    File annot_gff
+
+    String docker
+    String cluster_config
+    String disk_size
+
+    String out_dir = sample_id+'_BamQC'
+
+    command <<<
+        set -o pipefail
+        set -exo
+        nt=$(nproc)
+        /opt/qualimap/qualimap bamqc -bam ${bam_file} -gff ${annot_gff} -outformat PDF:HTML -nt $nt -outdir ${out_dir} --java-mem-size=32G
+        tar -zcvf ${out_dir}.tar ${out_dir}
+    >>>
+
+    runtime{
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output{
+        File out_file = "${out_dir}.tar"
+    }
+}