first commit

defaults

+{   
+    "host_image":"oss://database-shao/pathseq_database/pathseq_host.fa.img",
+    "host_kmer":"oss://database-shao/pathseq_database/pathseq_host.bfi",
+    "microbe_dict":"oss://database-shao/pathseq_database/pathseq_microbe.dict",
+    "microbe_bwa_image":"oss://database-shao/pathseq_database/pathseq_microbe.fa.img",
+    "microbe_taxonomy":"oss://database-shao/pathseq_database/pathseq_taxonomy.db",
+    "pathseq_docker":"registry.cn-shanghai.aliyuncs.com/shaolab_docker/gatk4:4.2.6.1",
+    "pathseq_cluster":"OnDemand bcs.ps.r.2xlarge img-ubuntu-vpc",
+    "disk_size":"300",
+    "fastp_docker":"registry.cn-shanghai.aliyuncs.com/shaolab_docker/teprof:1.5",
+    "fastp_cluster":"OnDemand bcs.ps.r.2xlarge 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"
+}

inputs

+{
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ project_name }}.fastq1": "{{ fastq1 }}",
+    "{{ project_name }}.fastq2": "{{ fastq2 }}",
+    "{{ project_name }}.host_image": "{{ host_image }}",
+    "{{ project_name }}.host_kmer": "{{ host_kmer }}",
+    "{{ project_name }}.microbe_dict": "{{ microbe_dict }}",
+    "{{ project_name }}.microbe_bwa_image": "{{ microbe_bwa_image }}",
+    "{{ project_name }}.microbe_taxonomy": "{{ microbe_taxonomy }}",
+    "{{ project_name }}.pathseq_docker": "{{ pathseq_docker }}",
+    "{{ project_name }}.pathseq_cluster": "{{ pathseq_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 }}"
+}

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 8 --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 8 -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 8 -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/pathseq.wdl

+task pathseq {
+    String sample_id
+    File fastq1
+    File fastq2
+    File host_image
+    File host_kmer
+    File microbe_dict
+    File microbe_bwa_image
+    File microbe_taxonomy
+
+    String disk_size
+    String docker
+    String cluster
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir ubam
+        mkdir filter_log
+        mkdir clean_pair_bam
+        mkdir clean_unpaired_bam
+        mkdir pathseq_result
+        mkdir bwa_pair_bam
+        mkdir bwa_pair_unpair_bam
+
+        gatk FastqToSam \
+            -F1 ${fastq1} \
+            -F2 ${fastq2} \
+            -O ./ubam/${sample_id}.bam \
+            -SM ${sample_id}
+
+        time gatk --java-options "-Xmx58g" PathSeqFilterSpark  \
+            --input ./ubam/${sample_id}.bam \
+            --paired-output ./clean_pair_bam/${sample_id}_paired.bam \
+            --unpaired-output ./clean_unpaired_bam/${sample_id}_unpaired.bam \
+            --min-clipped-read-length 70 \
+            --kmer-file ${host_kmer} \
+            --filter-bwa-image ${host_image} \
+            --filter-metrics filter_log/${sample_id}.log 
+
+        time gatk --java-options "-Xmx58g" PathSeqBwaSpark  \
+            --paired-input ./clean_pair_bam/${sample_id}_paired.bam \
+            --unpaired-input ./clean_unpaired_bam/${sample_id}_unpaired.bam \
+            --paired-output bwa_pair_bam/${sample_id}_bwa_paired.bam \
+            --unpaired-output bwa_unpair_bam/${sample_id}_bwa_unpaired.bam \
+            --microbe-bwa-image ${microbe_bwa_image} \
+            --microbe-dict ${microbe_dict}
+
+
+        time gatk --java-options "-Xmx58g" PathSeqScoreSpark  \
+            --paired-input bwa_pair_bam/${sample_id}_bwa_paired.bam \
+            --unpaired-input bwa_unpair_bam/${sample_id}_bwa_unpaired.bam \
+            --taxonomy-file ${microbe_taxonomy} \
+            --scores-output pathseq_result/${sample_id}.pathseq.txt \
+            --output pathseq_result/${sample_id}.pathseq_reads.bam \
+            --min-score-identity 0.90 \
+            --identity-margin 0.02
+
+        
+
+    >>>
+	
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File pathseq_txt = "pathseq_result/${sample_id}.pathseq.txt"
+        File pathseq_bam = "pathseq_result/${sample_id}.pathseq_reads.bam"
+        File pathseq_sbi = "pathseq_result/${sample_id}.pathseq_reads.bam.sbi"
+    }
+
+}
+

workflow.wdl

+import "./tasks/fastp.wdl" as fastp
+import "./tasks/pathseq.wdl" as pathseq
+
+workflow {{ project_name }} {
+    String sample_id
+    File fastq1
+    File fastq2
+    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 host_image
+    File host_kmer
+    File microbe_dict
+    File microbe_bwa_image
+    File microbe_taxonomy
+
+    String pathseq_docker
+    String pathseq_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 pathseq.pathseq as pathseq {
+                input:
+                sample_id=sample_id,
+                fastq1=fastp.Trim_R1,
+                fastq2=fastp.Trim_R2,
+                host_image=host_image,
+                host_kmer=host_kmer,
+                microbe_dict=microbe_dict,
+                microbe_bwa_image=microbe_bwa_image,
+                microbe_taxonomy=microbe_taxonomy,
+                disk_size=disk_size,
+                docker=pathseq_docker,
+                cluster=pathseq_cluster
+        }
+
+
+
+}