add fastp and revise samtools thread

defaults

 {
     "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/", 
-    "gtf": "oss://pgx-reference-data/reference/tophat2/annotation/gencode.v22.annotation.gtf",
+    "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
     "idx_prefix": "genome_snp_tran",
     "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
     "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
     "fastqscreen_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
     "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
     "fastqc_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+    "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
+    "fastp_cluster": "OnDemand bcs.a2.xlarge 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",
     "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",
     "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
     "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",

inputs

     "{{ project_name }}.fastqscreen_cluster": "{{ fastqscreen_cluster }}",
     "{{ project_name }}.fastqc_cluster": "{{ fastqc_cluster }}",
     "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
+    "{{ 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 }}.hisat2_docker": "{{ hisat2_docker }}",
     "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
     "{{ project_name }}.insert_size": "{{ insert_size }}",
     "{{ project_name }}.count_docker": "{{ count_docker }}",
     "{{ project_name }}.count_cluster": "{{ count_cluster }}",
     "{{ project_name }}.count_length": "{{ count_length }}",
-    "{{ project_name }}.pre_alignment_qc": "{{ pre_alignment_qc }}"
+    "{{ project_name }}.fastp_run": "{{ fastp_run }}",
+    "{{ project_name }}.pre_alignment_qc": "{{ pre_alignment_qc }}",
+    "{{ project_name }}.qualimap_qc": "{{ qualimap_qc }}"
 }

tasks/fastp.wdl

+task fastp {
+    String sample_id
+    File read1
+    File read2
+    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 <<<
+    nt=$(nproc)
+    mkdir -p /cromwell_root/tmp/fastp/
+	## 1.Disable_quality_filtering
+	if [ "${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 nt --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 nt -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 nt -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/hisat2.wdl

    File read_1P
    File read_2P
    String idx_prefix
-   String base=sub(basename(read_1P),"\\.\\S+$", "")
+   String sample_id
    String docker
    String cluster
    String disk_size
 
    command {
       nt=$(nproc)
-      hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam  --un-conc-gz ${base}_un.fq.gz
+      hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${sample_id}.sam  --un-conc-gz ${sample_id}_un.fq.gz
    }
    
    runtime { 
    }
 
    output {
-      File sam=base + ".sam"
-      File unmapread_1p=base + "_un.fq.1.gz"
-      File unmapread_2p=base + "_un.fq.2.gz"
+      File sam=sample_id + ".sam"
+      File unmapread_1p=sample_id + "_un.fq.1.gz"
+      File unmapread_2p=sample_id + "_un.fq.2.gz"
    }
 }

tasks/qualimap.wdl

 task qualimap {
 	File bam
-	File bam_percent
 	File gtf
 	String bamname=basename(bam, ".sorted.bam")
 	String docker

tasks/samtools.wdl

     String bam=base + ".bam"
     String sorted_bam=base + ".sorted.bam"
     String sorted_bam_index=base + ".sorted.bam.bai"
-    String percent_bam=base + ".percent.bam"
     String samstats=base + ".samstats"
     String ins_size=base + ".ins_size" 
     String docker
     command <<<
        set -o pipefail
        set -e
-       /opt/conda/bin/samtools view -bS ${sam} > ${bam}
-       /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
-       /opt/conda/bin/samtools index ${sorted_bam}
-       /opt/conda/bin/samtools view -bs 42.1 ${sorted_bam} > ${percent_bam}
-       /opt/conda/bin/samtools stats ${sorted_bam} > ${samstats}
-       /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size}
-
+       nt=$(nproc)
+       /opt/conda/bin/samtools view -@ nt -bS ${sam} > ${bam}
+       /opt/conda/bin/samtools sort -@ nt -m 2G ${bam} -o ${sorted_bam}
+       /opt/conda/bin/samtools index -@ nt ${sorted_bam}
+       /opt/conda/bin/samtools stats -@ nt ${sorted_bam} > ${samstats}
+       /opt/conda/bin/samtools stats -@ nt -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size}
     >>>
 
     runtime {
     }
 
     output {
-       File out_sort_bam=sorted_bam
-       File out_sort_bam_index=sorted_bam_index
-       File out_percent = percent_bam
-       File out_samstats=samstats
-       File out_ins_size=ins_size
+       File out_sort_bam="${sorted_bam}"
+       File out_sort_bam_index="${sorted_bam_index}"
+       File out_samstats="${samstats}"
+       File out_ins_size="${ins_size}"
     }
 
 }

workflow.wdl

 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/fastqscreen.wdl" as fastqscreen
+import "./tasks/fastp.wdl" as fastp
 import "./tasks/qualimap.wdl" as qualimap
 import "./tasks/hisat2.wdl" as hisat2
 import "./tasks/samtools.wdl" as samtools
 import "./tasks/count.wdl" as count
 
 workflow {{ project_name }} {
-
+	
 	File read1
 	File read2
 	File idx
 	String fastqc_cluster
 	String fastqscreen_docker
 	String fastqscreen_cluster
+	String fastp_docker
+	String fastp_cluster
+	String adapter_sequence
+	String adapter_sequence_r2
+	String umi_loc
 	String hisat2_docker
 	String hisat2_cluster
+	String idx_prefix
 	String stringtie_docker
 	String stringtie_cluster
 	String samtools_docker
 	String count_length
 	String sample_id
 
+	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
+
 	Boolean pre_alignment_qc
+	Boolean qualimap_qc
+	Boolean fastp_run
 	
 	if (pre_alignment_qc) {
 		
 		}	
 	}
 	
-	
-	call hisat2.hisat2 as hisat2 {
+	if (fastp_run){
+
+		call fastp.fastp as fastp {
+		input: 
+		sample_id=sample_id, 
+		read1=read1, 
+		read2=read2,
+		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 hisat2.hisat2 as hisat2 {
+		input: 
+		sample_id=sample_id, 
+		idx=idx, 
+		idx_prefix=idx_prefix, 
+		read_1P=fastp.Trim_R1, 
+		read_2P=fastp.Trim_R2,
+		docker=hisat2_docker,
+		cluster=hisat2_cluster,
+		disk_size=disk_size
+	}
+	} else {
+		call hisat2.hisat2 as hisat2 {
 		input: 
 		docker=hisat2_docker,
 		cluster=hisat2_cluster,
 		read_2P=read2,
 		disk_size=disk_size
 		}
-
+	}
+	
 	call samtools.samtools as samtools {
 		input: 
 		docker=samtools_docker,
 		disk_size=disk_size
 		}
 
-	call qualimap.qualimap as qualimap {
+	if (qualimap_qc){
+		call qualimap.qualimap as qualimap {
 		input:
 		bam=samtools.out_sort_bam,
-		bam_percent=samtools.out_percent,
 		gtf=gtf, 
 		docker=qualimap_docker,
 		cluster=qualimap_cluster,
 		disk_size=disk_size
 		}
+	}
 
 	call stringtie.stringtie as stringtie {
 		input: