first commit

README.md

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+word.docx

defaults

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+{   
+    "STAR_INDEX_DIR":"oss://database-shao/teprof_star_database/GRCh38.primary_assembly_gencode.25/",
+    "teprof_docker":"registry.cn-shanghai.aliyuncs.com/shaolab_docker/teprof:1.5",
+    "teprof_cluster":"OnDemand bcs.ps.g.2xlarge img-ubuntu-vpc",
+    "disk_size":"300",
+    "fastp_docker":"registry.cn-shanghai.aliyuncs.com/shaolab_docker/teprof:1.5",
+    "fastp_cluster":"OnDemand bcs.ps.g.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

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+{
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ project_name }}.fastq1": "{{ fastq1 }}",
+    "{{ project_name }}.fastq2": "{{ fastq2 }}",
+    "{{ project_name }}.STAR_INDEX_DIR": "{{ STAR_INDEX_DIR }}",
+    "{{ project_name }}.teprof_docker": "{{ teprof_docker }}",
+    "{{ project_name }}.teprof_cluster": "{{ teprof_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

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+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 32 --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 32 -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 32 -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/teprof_s1.wdl

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+task teprof_s1 {
+    String sample_id
+    File fastq1
+    File fastq2
+    File STAR_INDEX_DIR
+
+    String disk_size
+    String docker
+    String cluster
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+        pigz -p 8 -dc ${fastq1} > ${sample_id}_R1.fastq
+        pigz -p 8 -dc ${fastq2} > ${sample_id}_R2.fastq
+        STAR \
+            --runThreadN 8 \
+            --genomeDir ${STAR_INDEX_DIR} \
+            --readFilesIn ${sample_id}_R1.fastq ${sample_id}_R2.fastq \
+            --outSAMstrandField intronMotif \
+            --outSAMtype BAM SortedByCoordinate \
+            --outFileNamePrefix ./${sample_id}.
+
+       samtools view -@ 8 -q 255 -h ${sample_id}.Aligned.sortedByCoord.out.bam > ${sample_id}.filtered.Aligned.sortedByCoord.out.bam
+       stringtie -p 8 ${sample_id}.filtered.Aligned.sortedByCoord.out.bam -o ${sample_id}.Aligned.sortedByCoord.out.gtf -m 100 -c 1 --rf
+       python /database/rnapipelinerefhg38/rnapipeline/rmskhg38_annotate_gtf_update_test_tpm.py ${sample_id}.Aligned.sortedByCoord.out.gtf /database/rnapipelinerefhg38/rnapipeline/arguments.txt
+
+       python /database/rnapipelinerefhg38/rnapipeline/annotationtpmprocess.py ${sample_id}.Aligned.sortedByCoord.out.gtf_annotated_filtered_test
+       
+       mkdir ${sample_id}_annotated
+       cp ${sample_id}.Aligned.sortedByCoord.out.gtf_annotated_* ${sample_id}_annotated
+       tar -zcvf ${sample_id}_annotated.tgz ${sample_id}_annotated
+
+       rm ${sample_id}.filtered.Aligned.sortedByCoord.out.bam
+       rm ${sample_id}_R1.fastq
+       rm ${sample_id}_R2.fastq
+       
+
+    >>>
+	
+    runtime {
+        docker: docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File annotated = "${sample_id}_annotated.tgz"
+        File annotated_use = "${sample_id}.Aligned.sortedByCoord.out.gtf_annotated_filtered_test_c" 
+        File output_bam = "${sample_id}.Aligned.sortedByCoord.out.bam"
+        File output_gtf = "${sample_id}.Aligned.sortedByCoord.out.gtf"
+    }
+
+}
+

workflow_run.wdl

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+import "./tasks/fastp.wdl" as fastp
+import "./tasks/teprof_s1.wdl" as teprof_s1
+
+workflow run_teprof_s1 {
+    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 STAR_INDEX_DIR
+    String teprof_docker
+    String teprof_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 teprof_s1.teprof_s1 as teprof_s1 {
+                input:
+                sample_id=sample_id,
+                fastq1=fastp.Trim_R1,
+                fastq2=fastp.Trim_R2,
+                STAR_INDEX_DIR=STAR_INDEX_DIR,
+                disk_size=disk_size,
+                docker=teprof_docker,
+                cluster=teprof_cluster
+        }
+
+
+
+}