添加 'tasks'

tasks

@@ -0,0 +1,508 @@
+task bcftools {
+  
+  File ref_dir
+  String fasta
+  File vcf
+  String basename = basename(vcf,".vcf")
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    
+    # bcftools norm -m -both ${vcf} | bcftools norm -f ${ref_dir}/${fasta} -Ov -o ${basename}.norm.vcf
+    # Split multiallelic sites
+    bcftools norm -m -both ${vcf} -o ${basename}.norm.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File norm_vcf = "${basename}.norm.vcf"
+  }
+}
+task Sentieon_BQSR{
+    File ref_dir
+    File dbsnp_dir
+    File dbmills_dir
+
+    String sample_id
+    String ref_fasta
+    String dbsnp
+    String db_mills
+
+    File deduped_bam
+    File deduped_bam_index
+
+    # excute env
+    String docker
+    String cluster_config
+    String disk_size
+    
+    String SENTIEON_LICENSE
+
+    command<<<
+        set -o pipefail
+        set -exo
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        
+        nt=$(nproc)
+
+
+        sentieon driver -t $nt \
+        -r ${ref_dir}/${ref_fasta} -i ${deduped_bam} \
+        --algo QualCal \
+        -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
+        ${sample_id}_recal_data.table
+
+        sentieon driver -t $nt \
+        -r ${ref_dir}/${ref_fasta} -i ${deduped_bam} \
+        -q ${sample_id}_recal_data.table \
+        --algo QualCal \
+        -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
+        ${sample_id}_recal_data.table.post \
+        --algo ReadWriter ${sample_id}.sorted.deduped.recaled.bam
+
+        sentieon driver -t $nt --algo QualCal \
+        --plot --before ${sample_id}_recal_data.table --after ${sample_id}_recal_data.table.post ${sample_id}_recal_data.csv
+
+        sentieon plot bqsr -o ${sample_id}_bqsrreport.pdf ${sample_id}_recal_data.csv
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 250"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+
+    }
+
+    output{
+        File recal_table = "${sample_id}_recal_data.table"
+        File recal_post = "${sample_id}_recal_data.table.post"
+        File recaled_bam = "${sample_id}.sorted.deduped.recaled.bam"
+        File recaled_bam_index = "${sample_id}.sorted.deduped.recaled.bam.bai"
+        File recal_csv = "${sample_id}_recal_data.csv"
+        File bqsrreport_pdf = "${sample_id}_bqsrreport.pdf"
+
+    }
+}
+
+
+task fastp {
+    
+    # I/O options
+    File in1
+    File in2
+    String sample_id
+
+    Boolean? phred64 = false 
+    Boolean? fix_mgi_id = false
+
+    String? adapter_sequence
+    String? adapter_sequence_r2
+
+    Int? reads_to_process # specify how many reads/pairs to be processed. Default 0 means process all reads.
+
+    # reporting options
+    String json = sample_id+"fastp.json"
+    String html = sample_id+"fastp.html"
+    String report_title = "\'fastp report\'"
+
+    # excute env
+    String docker
+    String cluster_config
+    String disk_size
+
+    String out1_name = sample_id+'_clean_1.fastq'
+    String out2_name = sample_id+'_clean_2.fastq'
+
+    command <<<
+
+        # basic command
+        /opt/conda/bin/fastp \
+        --in1 ${in1} \
+        --in2 ${in2} \
+        --out1 ${out1_name} \
+        --out2 ${out2_name} \
+        --json ${json} \
+        --html ${html} \
+        --report_title ${report_title} \
+        
+        # options 
+        ${ true="--phred64 " false="" phred64 } \
+        ${ "--reads_to_process " + reads_to_process } \
+        ${ true="--fix_mgi_id " false="" fix_mgi_id } \
+        ${ "--adapter_sequence " + adapter_sequence } \
+        ${ "--adapter_sequence_r2 " + adapter_sequence_r2 }
+
+    >>>
+
+    runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File out1 = out1_name
+        File out2 = out2_name
+        File json_report = json
+        File html_report = html
+    }
+
+}
+
+task SentieonFastqToBam {
+    # 工具输入文件和参数
+    File fastq1
+    File fastq2
+    String sample_id
+    String Seq_platform
+    String ref_fasta
+    File ref_fasta_dir
+    String SENTIEON_LICENSE
+
+    String docker
+    String cluster_config
+    String disk_size
+
+    ## Extra driver parameters
+    String qc_driver_args = ""
+    String lc_driver_args = "--traverse_param=200000/10000"
+    String dedup_driver_args = "--traverse_param=200000/10000"
+    ## Extra algo parameters
+    String bwa_args = "-Y -M"
+    String bwa_chunk_size = "100000000"
+    String lc_args = ""
+    String bam_option = "--bam_compression 1"
+
+
+
+    
+    String out_bam = sample_id + ".dedup.bam"
+    String out_bai = sample_id + ".dedup.bam.bai"
+
+    # 工具运行命令
+    command <<<
+        set -exo pipefail
+        export SENTIEON_LICENSE=${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} ${out_bam} 
+         ls ./
+
+    >>>
+
+
+    runtime {
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+    }
+    
+
+    # 工具运行输出结果
+    output {
+        File deduped_bam = out_bam
+        File deduped_bam_bai = out_bai
+        Array[File] qc_metrics = glob("*_metrics.txt")
+    }
+
+}
+task manta_calling{
+    File tumor_bam
+    File tumor_bam_bai
+    File normal_bam
+    File normal_bam_bai
+    String ref_fasta
+    File ref_dir
+    String sample_id
+    
+    String docker
+    String cluster_config
+    String disk_size
+
+    
+    String out_dir = "${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"
+    }
+}
+
+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"
+    }
+}
+
+task strelka_calling{
+    File tumor_bam
+    File tumor_bam_bai
+    File normal_bam
+    File normal_bam_bai
+    String ref_fasta
+    File ref_dir
+    String sample_id
+    File manta_indel_vcf
+    File manta_indel_vcf_index
+    
+    String docker
+    String cluster_config
+    String disk_size
+
+    
+    String out_dir = "${sample_id}_result"
+    command <<<
+    set -exo pipefail
+    nt=$(nproc)
+    /home/biosoft/strelka-2.9.10.centos6_x86_64/bin/configureStrelkaSomaticWorkflow.py \
+    --normalBam ${normal_bam} \
+    --tumorBam ${tumor_bam} \
+    --referenceFasta ${ref_dir}/${ref_fasta} \
+    --indelCandidates ${manta_indel_vcf} \
+    --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"
+    }
+}
+task sentieon_TNscope{
+    String sample_id
+    File tumor_bam
+    File tumor_bam_bai
+    File? normal_bam
+    File? normal_bam_bai
+    String tumor_name
+    String normal_name
+    File tumor_recall_data
+    File normal_recall_data
+
+    File ref_dir
+    String ref_fasta
+    File dbsnp_dir
+    String dbsnp
+
+    # excute env
+    String docker
+    String cluster_config
+    String disk_size
+    String SENTIEON_LICENSE
+
+
+    command <<<
+        set -o pipefail
+        set -exo
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        nt=$(nproc)
+
+        sentieon driver -t $nt -r ${ref_dir}/${ref_fasta} \
+        -i ${tumor_bam} -q ${tumor_recall_data} \
+        -i ${normal_bam} -q ${normal_recall_data} \
+        --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+        --disable_detector sv --trim_soft_clip \
+        --dbsnp ${dbsnp_dir}/${dbsnp} ${sample_id}.TNscope.vcf || { echo "TNscope failed"; exit 1; }
+        
+        ls ./
+
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output{
+        File vcf = "${sample_id}.TNscope.vcf"
+        File vcf_index = "${sample_id}.TNscope.vcf.idx"
+
+    }
+}
+task sentieon_TNseq{
+    String sample_id
+    File tumor_bam
+    File tumor_bam_bai
+    File? normal_bam
+    File? normal_bam_bai
+    String tumor_name
+    String normal_name
+
+    File ref_dir
+    String ref_fasta
+    File germline_resource
+    File germline_resource_tbi
+
+    # excute env
+    String docker
+    String cluster_config
+    String disk_size
+    String SENTIEON_LICENSE
+
+
+    command <<<
+        set -o pipefail
+        set -exo
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        nt=$(nproc)
+
+
+        if [${normal_bam}];then
+            INPUT="-i ${tumor_bam} -i ${normal_bam}"
+            SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}"
+        else
+           INPUT="-i ${tumor_bam}"
+           SAMPLE="--tumor_sample ${tumor_name}"
+        fi
+
+        sentieon driver -t $nt -r ${ref_dir}/${ref_fasta} \
+        $INPUT \
+        --algo TNhaplotyper2 $SAMPLE \
+        --germline_vcf ${germline_resource} \
+        ${sample_id}.TNseq.raw.vcf \
+        --algo OrientationBias --tumor_sample ${tumor_name} \
+        ${sample_id}.orientation \
+        --algo ContaminationModel $SAMPLE \
+        --vcf ${germline_resource} \
+        --tumor_segments ${sample_id}.contamination.segments \
+        ${sample_id}.contamination
+
+        sentieon driver -t $nt \
+        -r ${ref_dir}/${ref_fasta} \
+        --algo TNfilter $SAMPLE \
+        -v ${sample_id}.TNseq.raw.vcf \
+        --contamination ${sample_id}.contamination \
+        --tumor_segments ${sample_id}.contamination.segments \
+        --orientation_priors ${sample_id}.orientation \
+        ${sample_id}.bwa_TNseq.vcf
+
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+    }
+
+    output{
+        File raw_vcf = "${sample_id}.TNseq.raw.vcf"
+        File raw_vcf_index = "${sample_id}.TNseq.raw.vcf.idx"
+        File vcf = "${sample_id}.bwa_TNseq.vcf"
+        File vcf_index = "${sample_id}.bwa_TNseq.vcf.idx"
+        File contamination = "${sample_id}.contamination"
+        File contamination_segments = "${sample_id}.contamination.segments"
+        File orientation = "${sample_id}.orientation"
+
+
+    }
+}