first commit

README.md

+word.docx

defaults

+{   
+    "starfusion_database_dir":"oss://pgx-reference-data/reference/starfusion/ctat_genome_lib_build_dir/",
+    "starfusion_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/starfusion:1.10.0",
+    "starfusion_cluster":"OnDemand bcs.b4.3xlarge img-ubuntu-vpc",
+    "disk_size":"200",
+    "fastp_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
+    "fastp_cluster":"OnDemand bcs.b4.3xlarge img-ubuntu-vpc",
+    "trim_front1":"0",
+    "trim_tail1":"0",
+    "max_len1":"0",
+    "trim_front2":"0",
+    "trim_tail2":"0",
+    "max_len2":"0",
+    "adapter_sequence":"AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
+    "adapter_sequence_r2":"AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
+    "disable_adapter_trimming":"0",
+    "length_required":"50",
+    "length_required1":"20",
+    "UMI":"0",
+    "umi_len":"0",
+    "umi_loc":"umi_loc",
+    "qualified_quality_phred":"20",
+    "disable_quality_filtering":"1",
+    "STAR_INDEX_DIR":"oss://pgx-reference-data/reference/arriba_hg38_v37/STAR_index_hg38_GENCODE37/",
+    "ASSEMBLY_FA":"oss://pgx-result/chenqingwang/arriba/hg38.fa",
+    "ANNOTATION_GTF":"oss://pgx-result/chenqingwang/arriba/GENCODE37.gtf",
+    "arriba_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/arriba:2.1.0",
+    "arriba_cluster":"OnDemand bcs.b4.3xlarge img-ubuntu-vpc",
+    "mixcr_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/mixcr:3",
+    "mixcr_cluster":"OnDemand bcs.b4.3xlarge img-ubuntu-vpc"
+}

inputs

+{
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ project_name }}.fastq1": "{{ fastq1 }}",
+    "{{ project_name }}.fastq2": "{{ fastq2 }}",
+    "{{ project_name }}.starfusion_database_dir": "{{ starfusion_database_dir }}",
+    "{{ project_name }}.starfusion_docker": "{{ starfusion_docker }}",
+    "{{ project_name }}.starfusion_cluster": "{{ starfusion_cluster }}",
+    "{{ project_name }}.disk_size": "{{ disk_size }}",
+    "{{ project_name }}.fastp_docker": "{{ fastp_docker }}",
+    "{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}",
+    "{{ project_name }}.trim_front1": "{{ trim_front1 }}",
+    "{{ project_name }}.trim_tail1": "{{ trim_tail1 }}",
+    "{{ project_name }}.max_len1": "{{ max_len1 }}",
+    "{{ project_name }}.trim_front2": "{{ trim_front2 }}",
+    "{{ project_name }}.trim_tail2": "{{ trim_tail2 }}",
+    "{{ project_name }}.max_len2": "{{ max_len2 }}",
+    "{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}",
+    "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
+    "{{ project_name }}.disable_adapter_trimming": "{{ disable_adapter_trimming }}",
+    "{{ project_name }}.length_required1": "{{ length_required1 }}",
+    "{{ project_name }}.UMI": "{{ UMI }}",
+    "{{ project_name }}.umi_loc": "{{ umi_loc }}",
+    "{{ project_name }}.umi_len": "{{ umi_len }}",
+    "{{ project_name }}.length_required": "{{ length_required }}",
+    "{{ project_name }}.qualified_quality_phred": "{{ qualified_quality_phred }}",
+    "{{ project_name }}.disable_quality_filtering": "{{ disable_quality_filtering }}",
+    "{{ project_name }}.STAR_INDEX_DIR": "{{ STAR_INDEX_DIR }}",
+    "{{ project_name }}.ASSEMBLY_FA": "{{ ASSEMBLY_FA }}",
+    "{{ project_name }}.ANNOTATION_GTF": "{{ ANNOTATION_GTF }}",
+    "{{ project_name }}.arriba_docker": "{{ arriba_docker }}",
+    "{{ project_name }}.arriba_cluster": "{{ arriba_cluster }}",
+    "{{ project_name }}.mixcr_docker": "{{ mixcr_docker }}",
+    "{{ project_name }}.mixcr_cluster": "{{ mixcr_cluster }}"
+}

tasks/arriba.wdl

+task arriba{
+    String sample_id
+    File fastq1
+    File fastq2
+    File STAR_INDEX_DIR
+    File ASSEMBLY_FA
+    File ANNOTATION_GTF
+
+    String disk_size
+    String docker
+    String cluster
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir ./output/
+        STAR \
+            --runThreadN 16 \
+            --genomeDir ${STAR_INDEX_DIR} \
+            --genomeLoad NoSharedMemory \
+            --readFilesIn ${fastq1} ${fastq2} \
+            --readFilesCommand zcat \
+            --outSAMtype BAM Unsorted \
+            --outSAMunmapped Within \
+            --outBAMcompression 0 \
+            --outFilterMultimapNmax 50 \
+            --peOverlapNbasesMin 10 \
+            --alignSplicedMateMapLminOverLmate 0.5 \
+            --alignSJstitchMismatchNmax 5 -1 5 5 \
+            --chimSegmentMin 10 \
+            --chimOutType WithinBAM HardClip \
+            --chimJunctionOverhangMin 10 \
+            --chimScoreDropMax 30 \
+            --chimScoreJunctionNonGTAG 0 \
+            --chimScoreSeparation 1 \
+            --chimSegmentReadGapMax 3 \
+            --chimMultimapNmax 50 \
+            --outFileNamePrefix ./output/${sample_id}.
+                  
+                  
+         /arriba_v2.1.0/arriba \
+            -x ./output/${sample_id}.Aligned.out.bam \
+            -o ./output/${sample_id}_fusions.tsv -O ./output/${sample_id}_fusions.discarded.tsv \
+            -a ${ASSEMBLY_FA} \
+            -g ${ANNOTATION_GTF} \
+            -b /arriba_v2.1.0/database/blacklist_hg38_GRCh38_v2.1.0.tsv.gz \
+            -k /arriba_v2.1.0/database/known_fusions_hg38_GRCh38_v2.1.0.tsv.gz \
+            -t /arriba_v2.1.0/database/known_fusions_hg38_GRCh38_v2.1.0.tsv.gz \
+            -p /arriba_v2.1.0/database/protein_domains_hg38_GRCh38_v2.1.0.gff3
+
+
+    >>>
+	
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] arriba_result=glob("./output/*.tsv")
+        Array[File] arriba_bam=glob("./output/*.bam")
+    }
+
+}
+
+

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 umi_loc	
+    Int trim_front1
+    Int trim_tail1
+    Int max_len1
+    Int trim_front2
+    Int trim_tail2
+    Int max_len2
+    Int disable_adapter_trimming
+    Int length_required
+    Int umi_len
+    Int UMI
+    Int qualified_quality_phred
+    Int length_required1
+    Int disable_quality_filtering
+   
+	command <<<
+        mkdir -p /cromwell_root/tmp/fastp/
+	##1.Disable_quality_filtering
+	if [ "${disable_quality_filtering}" == 0 ]
+        then
+	cp ${read1} /cromwell_root/tmp/fastp/{sample_id}_R1.fastq.tmp1.gz
+	cp ${read2} /cromwell_root/tmp/fastp/{sample_id}_R2.fastq.tmp1.gz
+        else
+	fastp --thread 16 --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i ${read1} -I ${read2} -o /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp1.gz -O /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp1.gz -j ${sample_id}.json -h ${sample_id}.html
+        fi
+
+	##2.UMI
+	if [ "${UMI}" == 0 ]
+        then
+	cp /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp1.gz /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz
+	cp /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp1.gz /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz
+        else
+	fastp --thread 16 -U --umi_loc=${umi_loc} --umi_len=${umi_len} --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp1.gz -I /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp1.gz -o /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz -O /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz -j ${sample_id}.json -h ${sample_id}.html
+	fi
+
+	##3.Trim
+        if [ "${disable_adapter_trimming}" == 0 ]
+        then
+	fastp --thread 16 -l ${length_required} -q ${qualified_quality_phred} -u ${length_required1} --adapter_sequence ${adapter_sequence} --adapter_sequence_r2 ${adapter_sequence_r2} --detect_adapter_for_pe --trim_front1 ${trim_front1} --trim_tail1 ${trim_tail1} --max_len1 ${max_len1} --trim_front2 ${trim_front2} --trim_tail2 ${trim_tail2} --max_len2 ${max_len2} -i /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz -I /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz -o ${sample_id}_R1.fastq.gz -O ${sample_id}_R2.fastq.gz -j ${sample_id}.json -h ${sample_id}.html
+        else
+	cp /cromwell_root/tmp/fastp/${sample_id}_R1.fastq.tmp2.gz ${sample_id}_R1.fastq.gz
+	cp /cromwell_root/tmp/fastp/${sample_id}_R2.fastq.tmp2.gz ${sample_id}_R2.fastq.gz
+        fi
+   >>>
+   
+   runtime { 
+		docker: docker
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+   }
+
+   output {
+      File json = "${sample_id}.json"
+      File report = "${sample_id}.html"
+      File Trim_R1 = "${sample_id}_R1.fastq.gz"
+      File Trim_R2 = "${sample_id}_R2.fastq.gz"
+   }
+}

tasks/mixcr.wdl

+task mixcr{
+    String sample_id
+    File fastq1
+    File fastq2
+	
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir  ${sample_id}_mixcr_output
+        mixcr analyze shotgun --species hs \
+            -t 16 \
+            --starting-material rna \
+            --only-productive ${fastq1} ${fastq2} ${sample_id}_mixcr_output/${sample_id}
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] mixcr_result=glob("${sample_id}_mixcr_output/${sample_id}*")
+    }
+
+}
+
+

tasks/starfusion.wdl

+task starfusion{
+    String sample_id
+    File fastq1
+    File fastq2
+    File database_dir
+	
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir -p ${sample_id}/output
+
+        STAR-Fusion --genome_lib_dir ${database_dir} \
+            --left_fq ${fastq1} \
+            --right_fq ${fastq2} \
+            --CPU 16 \
+            --output_dir  ${sample_id}/output \
+            --FusionInspector validate \
+            --examine_coding_effect
+
+
+        tar -zcvf ${sample_id}/output/${sample_id}_FusionInspector-validate.tgz ${sample_id}/output/FusionInspector-validate
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] starfusion_result=glob("${sample_id}/output/*.tsv")
+        Array[File] FusionInspector_result=glob("${sample_id}/output/FusionInspector-validate/*.tsv")
+        Array[File] starfusion_bam=glob("${sample_id}/output/*.bam")
+        Array[File] starfusion_tab=glob("${sample_id}/output/*.tab")
+        Array[File] starfusion_junction=glob("${sample_id}/output/*.junction")
+        Array[File] starfusion_out=glob("${sample_id}/output/*.out")
+        Array[File] starfusion_tgz=glob("${sample_id}/output/*.tgz")
+    }
+
+}
+
+

workflow.wdl

+import "./tasks/starfusion.wdl" as starfusion
+import "./tasks/fastp.wdl" as fastp
+import "./tasks/arriba.wdl" as arriba
+import "./tasks/mixcr.wdl" as mixcr
+
+workflow {{ project_name }} {
+    String sample_id
+    File fastq1
+    File fastq2
+    File starfusion_database_dir
+    String starfusion_docker
+    String starfusion_cluster
+    String disk_size
+
+    String fastp_docker
+    String fastp_cluster
+    String adapter_sequence
+    String adapter_sequence_r2
+    String umi_loc
+    Int trim_front1
+    Int trim_tail1
+    Int max_len1
+    Int trim_front2
+    Int trim_tail2
+    Int max_len2
+    Int disable_adapter_trimming
+    Int length_required
+    Int umi_len
+    Int UMI
+    Int qualified_quality_phred
+    Int length_required1
+    Int disable_quality_filtering
+    
+    File STAR_INDEX_DIR
+    File ASSEMBLY_FA
+    File ANNOTATION_GTF
+    String arriba_docker
+    String arriba_cluster
+
+    String mixcr_docker
+    String mixcr_cluster
+
+
+        call fastp.fastp as fastp {
+                input:
+                read1=fastq1,
+                read2=fastq2,
+                sample_id=sample_id,
+                docker=fastp_docker,
+                cluster=fastp_cluster,
+                disk_size=disk_size,
+                adapter_sequence=adapter_sequence,
+                adapter_sequence_r2=adapter_sequence_r2,
+                umi_loc=umi_loc,
+                trim_front1=trim_front1,
+                trim_tail1=trim_tail1,
+                max_len1=max_len1,
+                trim_front2=trim_front2,
+                trim_tail2=trim_tail2,
+                max_len2=max_len2,
+                disable_adapter_trimming=disable_adapter_trimming,
+                length_required=length_required,
+                umi_len=umi_len,
+                UMI=UMI,
+                qualified_quality_phred=qualified_quality_phred,
+                length_required1=length_required1,
+                disable_quality_filtering=disable_quality_filtering
+        }
+
+        call starfusion.starfusion as starfusion {
+                input:	
+                sample_id=sample_id,
+                fastq1=fastp.Trim_R1,
+                fastq2=fastp.Trim_R2,
+                database_dir=starfusion_database_dir,
+                docker=starfusion_docker,
+                cluster=starfusion_cluster,
+                disk_size=disk_size
+
+        }
+
+        call arriba.arriba as arriba {
+                input:
+                sample_id=sample_id,
+                fastq1=fastp.Trim_R1,
+                fastq2=fastp.Trim_R2,
+                STAR_INDEX_DIR=STAR_INDEX_DIR,
+                ASSEMBLY_FA=ASSEMBLY_FA,
+                ANNOTATION_GTF=ANNOTATION_GTF,
+                disk_size=disk_size,
+                docker=arriba_docker,
+                cluster=arriba_cluster
+        }
+
+        call mixcr.mixcr as mixcr {
+                input:
+                sample_id=sample_id,
+                fastq1=fastp.Trim_R1,
+                fastq2=fastp.Trim_R2,
+                docker=mixcr_docker,
+                cluster=mixcr_cluster,
+                disk_size=disk_size
+
+        }
+
+
+}