update

defaults

@@ -1,17 +1,17 @@
 {
-    "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
-    "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:0.11.8",
-    "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
-    "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
-    "CPU2_GB8_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
-    "CPU4_GB16_cluster": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
-    "CPU8_GB32_cluster": "OnDemand bcs.ps.g.2xlarge img-ubuntu-vpc",
-    "disk_size": "300",
-    "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-    "SENTIEON_LICENSE": "192.168.0.55:8990",
-    "covered_bed": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
-    "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
-    "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
-    "fasta": "GRCh38.d1.vd1.fa",
-    "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+  "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
+  "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:0.11.8",
+  "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+  "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
+  "CPU2_GB8_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",
+  "CPU4_GB16_cluster": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
+  "CPU8_GB32_cluster": "OnDemand bcs.ps.g.2xlarge img-ubuntu-vpc",
+  "disk_size": "300",
+  "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "SENTIEON_LICENSE": "192.168.0.55:8990",
+  "covered_bed": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
+  "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
+  "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
+  "fasta": "GRCh38.d1.vd1.fa",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
 }

tasks/Dedup.wdl

@@ -1,39 +1,39 @@
 task Dedup {
 
-    String SENTIEON_INSTALL_DIR
-    String SENTIEON_LICENSE
-    String sample
-    File sorted_bam
-    File sorted_bam_index
-    
-    String docker
-    String cluster_config
-    String disk_size
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String sample
+  File sorted_bam
+  File sorted_bam_index
+  
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        set -o pipefail
-        set -e
-        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-        nt=$(nproc)
-        ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
-        ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam
-        sed -n '3p' ${sample}_dedup_metrics.txt | awk -F'\t' '{print "'"${sample}"'""\t"$9*100}' > ${sample}_picard_duplication.txt
-        # ${sample}_marked_dup_metrics.txt can be recognized as the picard output
-        sed '1i\#DuplicationMetrics' ${sample}_dedup_metrics.txt > ${sample}_marked_dup_metrics.txt
-    >>>
-    
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam
+    sed -n '3p' ${sample}_dedup_metrics.txt | awk -F'\t' '{print "'"${sample}"'""\t"$9*100}' > ${sample}_picard_duplication.txt
+    # ${sample}_marked_dup_metrics.txt can be recognized as the picard output
+    sed '1i\#DuplicationMetrics' ${sample}_dedup_metrics.txt > ${sample}_marked_dup_metrics.txt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-    output {
-        File score = "${sample}_score.txt"
-        File dedup_metrics = "${sample}_marked_dup_metrics.txt"
-        File duplication = "${sample}_picard_duplication.txt"
-        File deduped_bam = "${sample}.sorted.deduped.bam"
-        File deduped_bam_index = "${sample}.sorted.deduped.bam.bai"
-    }
+  output {
+    File score = "${sample}_score.txt"
+    File dedup_metrics = "${sample}_marked_dup_metrics.txt"
+    File duplication = "${sample}_picard_duplication.txt"
+    File deduped_bam = "${sample}.sorted.deduped.bam"
+    File deduped_bam_index = "${sample}.sorted.deduped.bam.bai"
+  }
 }

tasks/Metrics.wdl

@@ -1,49 +1,65 @@
 task Metrics {
 
-    File ref_dir
-    String SENTIEON_INSTALL_DIR
-    String SENTIEON_LICENSE
-    String sample
-    String fasta
-    File sorted_bam
-    File sorted_bam_index
-    
-    String docker
-    String cluster_config
-    String disk_size
+  File ref_dir
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String sample
+  String docker
+  String cluster_config
+
+  String fasta
+  File sorted_bam
+  File sorted_bam_index
+  String disk_size
 
-    command <<<
-        set -o pipefail
-        set -e
-        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-        nt=$(nproc)
-        ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${sorted_bam} --algo MeanQualityByCycle ${sample}_mq_metrics.txt --algo QualDistribution ${sample}_qd_metrics.txt --algo GCBias --summary ${sample}_gc_summary.txt ${sample}_gc_metrics.txt --algo AlignmentStat ${sample}_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_is_metrics.txt --algo CoverageMetrics --omit_base_output ${sample}_coverage_metrics
+  File? regions
 
-        ${SENTIEON_INSTALL_DIR}/bin/sentieon plot metrics -o ${sample}_metrics_report.pdf gc=${sample}_gc_metrics.txt qd=${sample}_qd_metrics.txt mq=${sample}_mq_metrics.txt isize=${sample}_is_metrics.txt
-    >>>
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions}"
+    else
+      INTERVAL=""
+    fi
     
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    output {
-        File qd_metrics = "${sample}_qd_metrics.txt"
-        File qd_metrics_pdf = "${sample}_qd_metrics.pdf"
-        File mq_metrics = "${sample}_mq_metrics.txt"
-        File mq_metrics_pdf = "${sample}_mq_metrics.pdf"
-        File is_metrics = "${sample}_is_metrics.txt"
-        File is_metrics_pdf = "${sample}_is_metrics.pdf"
-        File gc_summary = "${sample}_gc_summary.txt"
-        File gc_metrics = "${sample}_gc_metrics.txt"
-        File gc_metrics_pdf = "${sample}_gc_metrics.pdf"
-        File aln_metrics = "${sample}_aln_metrics.txt"
-        File coverage_metrics_sample_summary = "${sample}_coverage_metrics.sample_summary"
-        File coverage_metrics_sample_statistics = "${sample}_coverage_metrics.sample_statistics"
-        File coverage_metrics_sample_interval_statistics = "${sample}_coverage_metrics.sample_interval_statistics"
-        File coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_coverage_metrics.sample_cumulative_coverage_proportions"
-        File coverage_metrics_sample_cumulative_coverage_counts = "${sample}_coverage_metrics.sample_cumulative_coverage_counts"
-    }
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} $INTERVAL \
+    -i ${sorted_bam} \
+    --algo MeanQualityByCycle ${sample}_mq_metrics.txt \
+    --algo QualDistribution ${sample}_qd_metrics.txt \
+    --algo GCBias --summary ${sample}_gc_summary.txt ${sample}_gc_metrics.txt \
+    --algo AlignmentStat ${sample}_aln_metrics.txt \
+    --algo InsertSizeMetricAlgo ${sample}_is_metrics.txt \
+    --algo CoverageMetrics --omit_base_output ${sample}_coverage_metrics
 
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon plot metrics -o ${sample}_metrics_report.pdf gc=${sample}_gc_metrics.txt qd=${sample}_qd_metrics.txt mq=${sample}_mq_metrics.txt isize=${sample}_is_metrics.txt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File qd_metrics = "${sample}_qd_metrics.txt"
+    File qd_metrics_pdf = "${sample}_qd_metrics.pdf"
+    File mq_metrics = "${sample}_mq_metrics.txt"
+    File mq_metrics_pdf = "${sample}_mq_metrics.pdf"
+    File is_metrics = "${sample}_is_metrics.txt"
+    File is_metrics_pdf = "${sample}_is_metrics.pdf"
+    File gc_summary = "${sample}_gc_summary.txt"
+    File gc_metrics = "${sample}_gc_metrics.txt"
+    File gc_metrics_pdf = "${sample}_gc_metrics.pdf"
+    File aln_metrics = "${sample}_aln_metrics.txt"
+    File coverage_metrics_sample_summary = "${sample}_coverage_metrics.sample_summary"
+    File coverage_metrics_sample_statistics = "${sample}_coverage_metrics.sample_statistics"
+    File coverage_metrics_sample_interval_statistics = "${sample}_coverage_metrics.sample_interval_statistics"
+    File coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_coverage_metrics.sample_cumulative_coverage_proportions"
+    File coverage_metrics_sample_cumulative_coverage_counts = "${sample}_coverage_metrics.sample_cumulative_coverage_counts"
+  }
 }

tasks/deduped_Metrics.wdl

@@ -1,45 +1,63 @@
 task deduped_Metrics {
 
-    File ref_dir
-    String SENTIEON_INSTALL_DIR
-    String SENTIEON_LICENSE
-    String sample
-    String fasta
-    File deduped_bam
-    File deduped_bam_index
-    
-    String docker
-    String cluster_config
-    String disk_size
-    
-    command <<<
-        set -o pipefail
-        set -e
-        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-        nt=$(nproc)
-        ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${deduped_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt --algo QualityYield ${sample}_deduped_QualityYield.txt --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
-    >>>
+  File ref_dir
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String sample
+  String fasta
+  File deduped_bam
+  File deduped_bam_index
+  String docker
+  String cluster_config
+  String disk_size
 
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
-    }
+  File? regions
 
-    output {
-        File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
-        File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
-        File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
-        File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
-        File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
-		File deduped_mean_quality = "${sample}_deduped_mq_metrics.txt"
-		File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
-		File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
-		File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
-		File dedeuped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
-		File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
-        File deduped_QualityYield = "${sample}_deduped_QualityYield.txt"
-		File deduped_wgsmetrics = "${sample}_deduped_WgsMetricsAlgo.txt"
-    }
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+
+    if [ ${regions} ]; then
+      INTERVAL="--interval ${regions}"
+    else
+      INTERVAL=""
+    fi
+
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} $INTERVAL \
+    -i ${deduped_bam} \
+    --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics \
+    --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt \
+    --algo QualDistribution ${sample}_deduped_qd_metrics.txt \
+    --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt \
+    --algo AlignmentStat ${sample}_deduped_aln_metrics.txt \
+    --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt \
+    --algo QualityYield ${sample}_deduped_QualityYield.txt \
+    --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
+  }
+
+  output {
+    File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
+    File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
+    File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
+    File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
+    File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
+    File deduped_mean_quality = "${sample}_deduped_mq_metrics.txt"
+    File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
+    File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
+    File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
+    File dedeuped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
+    File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
+    File deduped_QualityYield = "${sample}_deduped_QualityYield.txt"
+    File deduped_wgsmetrics = "${sample}_deduped_WgsMetricsAlgo.txt"
+  }
 }

tasks/fastqc.wdl

@@ -1,33 +1,33 @@
 task fastqc {
-    
-    String sample
-    File read1
-    File read2
-    
-    String docker
-    String cluster_config
-    String disk_size
+  
+  String sample
+  File read1
+  File read2
+  
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        set -o pipefail
-        set -e
-        nt=$(nproc)
-        ln -s ${read1} ${sample}_R1.fastq.gz
-        ln -s ${read2} ${sample}_R2.fastq.gz
-        fastqc -t $nt -o ./ ${sample}_R1.fastq.gz
-        fastqc -t $nt -o ./ ${sample}_R2.fastq.gz
-    >>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    ln -s ${read1} ${sample}_R1.fastq.gz
+    ln -s ${read2} ${sample}_R2.fastq.gz
+    fastqc -t $nt -o ./ ${sample}_R1.fastq.gz
+    fastqc -t $nt -o ./ ${sample}_R2.fastq.gz
+  >>>
 
-    runtime {
-        docker:docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    output {
-        File read1_html="${sample}_R1_fastqc.html"
-        File read1_zip="${sample}_R1_fastqc.zip"
-        File read2_html="${sample}_R2_fastqc.html"
-        File read2_zip="${sample}_R2_fastqc.zip"
-    }
+  runtime {
+    docker:docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File read1_html="${sample}_R1_fastqc.html"
+    File read1_zip="${sample}_R1_fastqc.zip"
+    File read2_html="${sample}_R2_fastqc.html"
+    File read2_zip="${sample}_R2_fastqc.zip"
+  }
 }

tasks/fastqscreen.wdl

@@ -1,40 +1,40 @@
 task fastq_screen {
-    
-    String sample
-    File read1
-    File read2
-    File screen_ref_dir
-    File fastq_screen_conf
+  
+  String sample
+  File read1
+  File read2
+  File screen_ref_dir
+  File fastq_screen_conf
 
-    String docker
-    String cluster_config
-    String disk_size
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        set -o pipefail
-        set -e
-        nt=$(nproc)
-        mkdir -p /cromwell_root/tmp
-        cp -r ${screen_ref_dir} /cromwell_root/tmp/
-        ln -s ${read1} ${sample}_R1.fastq.gz
-        ln -s ${read2} ${sample}_R2.fastq.gz
-        fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R1.fastq.gz
-        fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R2.fastq.gz
-    >>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    mkdir -p /cromwell_root/tmp
+    cp -r ${screen_ref_dir} /cromwell_root/tmp/
+    ln -s ${read1} ${sample}_R1.fastq.gz
+    ln -s ${read2} ${sample}_R2.fastq.gz
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R1.fastq.gz
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R2.fastq.gz
+  >>>
 
-    runtime {
-        docker:docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
+  runtime {
+    docker:docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-    output {
-        File png1 = "${sample}_R1_screen.png"
-        File txt1 = "${sample}_R1_screen.txt"
-        File html1 = "${sample}_R1_screen.html"
-        File png2 = "${sample}_R2_screen.png"
-        File txt2 = "${sample}_R2_screen.txt"
-        File html2 = "${sample}_R2_screen.html"
-    }
+  output {
+    File png1 = "${sample}_R1_screen.png"
+    File txt1 = "${sample}_R1_screen.txt"
+    File html1 = "${sample}_R1_screen.html"
+    File png2 = "${sample}_R2_screen.png"
+    File txt2 = "${sample}_R2_screen.txt"
+    File html2 = "${sample}_R2_screen.html"
+  }
 }

tasks/mapping.wdl

@@ -1,36 +1,36 @@
 task mapping {
-    
-    String sample
-    File fastq_1
-    File fastq_2
+  
+  String sample
+  File fastq_1
+  File fastq_2
 
-    String SENTIEON_INSTALL_DIR
-    String SENTIEON_LICENSE
-    String group
-    String pl
-    File ref_dir
-    String fasta
-    
-    String docker
-    String cluster_config
-    String disk_size
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String group
+  String pl
+  File ref_dir
+  String fasta
+  
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        set -o pipefail
-        set -e	
-        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-        nt=$(nproc)
-        ${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
-    >>>
+  command <<<
+    set -o pipefail
+    set -e	
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    ${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
+  >>>
 
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    output {
-        File sorted_bam = "${sample}.sorted.bam"
-        File sorted_bam_index = "${sample}.sorted.bam.bai"
-    }
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File sorted_bam = "${sample}.sorted.bam"
+    File sorted_bam_index = "${sample}.sorted.bam.bai"
+  }
 }

tasks/qualimap.wdl

@@ -1,33 +1,33 @@
 task qualimap {
-    
-    String sample
-    File bam
-    File bai
-    File covered_bed
-    
-    String docker
-    String cluster_config
-    String disk_size
+  
+  String sample
+  File bam
+  File bai
+  File covered_bed
+  
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        set -o pipefail
-        set -e
-        nt=$(nproc)
-        awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${covered_bed} > new.bed
-        /opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${sample} --java-mem-size=32G
-        cat ${sample}/genome_results.txt | grep duplication | awk -F "= |%" '{print "'"${sample}"'""\t"$2}' > ${sample}_qualimap_duplication.txt
-        tar -zcvf ${sample}_qualimap.tar ${sample}
-    >>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${covered_bed} > new.bed
+    /opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${sample} --java-mem-size=32G
+    cat ${sample}/genome_results.txt | grep duplication | awk -F "= |%" '{print "'"${sample}"'""\t"$2}' > ${sample}_qualimap_duplication.txt
+    tar -zcvf ${sample}_qualimap.tar ${sample}
+  >>>
 
-    runtime {
-        docker:docker
-        cluster:cluster_config
-        systemDisk:"cloud_ssd 40"
-        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    
-    output {
-        File tar = "${sample}_qualimap.tar"
-        File duplication = "${sample}_qualimap_duplication.txt"
-    }
+  runtime {
+    docker:docker
+    cluster:cluster_config
+    systemDisk:"cloud_ssd 40"
+    dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File tar = "${sample}_qualimap.tar"
+    File duplication = "${sample}_qualimap_duplication.txt"
+  }
 }

workflow.wdl

@@ -5,8 +5,6 @@ import "./tasks/mapping.wdl" as mapping
 import "./tasks/Metrics.wdl" as Metrics
 import "./tasks/Dedup.wdl" as Dedup
 import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
-import "./tasks/Realigner.wdl" as Realigner
-import "./tasks/BQSR.wdl" as BQSR
 
 
 workflow {{ project_name }} {
@@ -78,6 +76,7 @@ workflow {{ project_name }} {
     sorted_bam=mapping.sorted_bam,
     sorted_bam_index=mapping.sorted_bam_index,
     sample=sample_id,
+    regions=covered_bed,
     docker=sentieon_docker,
     disk_size=disk_size,
     cluster_config=CPU2_GB8_cluster
@@ -104,6 +103,7 @@ workflow {{ project_name }} {
     deduped_bam=Dedup.deduped_bam,
     deduped_bam_index=Dedup.deduped_bam_index,
     sample=sample_id,
+    regions=covered_bed,
     docker=sentieon_docker,
     disk_size=disk_size,
     cluster_config=CPU2_GB8_cluster
@@ -119,40 +119,6 @@ workflow {{ project_name }} {
     disk_size=disk_size,
     cluster_config=CPU8_GB32_cluster
   }
-  
-  call Realigner.Realigner as Realigner {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    deduped_bam=Dedup.deduped_bam,
-    deduped_bam_index=Dedup.deduped_bam_index,
-    db_mills=db_mills,
-    dbmills_dir=dbmills_dir,
-    sample=sample_id + '_tumor',
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
-  }
-
-  call BQSR.BQSR as BQSR {
-    input:
-    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-    SENTIEON_LICENSE=SENTIEON_LICENSE,
-    fasta=fasta,
-    ref_dir=ref_dir,
-    realigned_bam=Realigner.realigner_bam,
-    realigned_bam_index=Realigner.realigner_bam_index,
-    db_mills=db_mills,
-    dbmills_dir=dbmills_dir,
-    dbsnp=dbsnp,
-    dbsnp_dir=dbsnp_dir,
-    sample=sample_id + '_tumor',
-    docker=sentieon_docker,
-    disk_size=disk_size,
-    cluster_config=cluster_config
-  }
 
   output {
     File fastqc_read1_html = fastqc.read1_html