PeakSnake/Snakefile

import os
import yaml

configfile: "config.yaml"
##########################################################
# 全局变量和样本信息
##########################################################
## 软件主目录
PEAKSNAKE_HOME = config["PEAKSNAKE_HOME"] if config["PEAKSNAKE_HOME"] else os.getcwd()
PEAK_TYPE = config["peak_type"]
SEQ_TYPE = config["seq_type"]
PEAK_SELECTION = config["peak_selection"]
GENOME = config["genome"]
GTF = config["gtf"]

## 样本信息变量
# 字典:REPLICATE to INPUT 
REPLICATE_TO_INPUT = {k: config['samples'][k] for k in sorted(config['samples'])}

# 列表:所有 REPLICATES 
REPLICATES = sorted(list(set(REPLICATE_TO_INPUT.keys())))
# 列表:所有 INPUTS 
INPUTS = sorted(list(set(REPLICATE_TO_INPUT.values())))
INPUTS = [] if INPUTS == [None] else INPUTS

# 字典: SAMPLE 与 rep1 rep2 rep2 对应关系
SAMPLE_TO_REPLICATE = {}
for s in REPLICATES:
    name, rep = '_'.join(s.split('_')[:-1]), s.split('_')[-1]
    SAMPLE_TO_REPLICATE.setdefault(name, []).append(rep)

SAMPLE_TO_REPLICATE = {k: sorted(v) for k, v in SAMPLE_TO_REPLICATE.items()}

## 生成样本信息表
with open("sample_sheet.csv", 'w') as f:
    f.write("SampleID,ControlID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,Peaks,bamControl,PeakCaller\n")

    for sample, control in REPLICATE_TO_INPUT.items():
        sample_parts = sample.split('_')
        factor = sample_parts[0]  # 提取样本ID中的Factor
        tissue = "NA"
        treatment = sample_parts[1]  # 在这个例子中，tissue和condition是相同的
        condition = factor + "_" + treatment
        replicate = sample_parts[2].replace("rep", "")  # 将"rep1"和"rep2"转换为"1"和"2"

        if control:
            control_parts = control.split('_')
            control_id = "_".join(control_parts[:2])  # 构建 ControlID
            bamControl = f"clean_bams/{control}_final.bam"
        else:
            control_id = "NA"
            bamControl = "NA"

        bamReads = f"clean_bams/{sample}_final.bam"
        peaks = f"clean_peaks/cutoff/{sample}_peaks.{PEAK_TYPE}Peak"

        f.write(f"{sample},{control_id},{tissue},{factor},{condition},{treatment},{replicate},{bamReads},{peaks},{bamControl},bed\n")

##########################################################
# rule all: 最终想要生成的文件 
##########################################################
rule all:
    input:
	#####################################
	# 从 fastq 到 peaks 
	#####################################
        # 最终比对结果
        expand("clean_bams/{replicate}_final.bam", replicate = REPLICATES + INPUTS),
        # bw 文件, deeptools 可视化
        expand("clean_bams/{replicate}.bw", replicate = REPLICATES + INPUTS),
        "deeptools/sample_correlation.pdf" if len(REPLICATES) > 2 else [],
        "deeptools/tss_heatmap.pdf",
        "deeptools/tss_tes_heatmap.pdf",
        # raw peak 结果
        expand("raw_peaks/{replicate}_peaks.{PEAK_TYPE}Peak", replicate = REPLICATES, PEAK_TYPE = PEAK_TYPE),
        # cutoff analysis
        expand("raw_peaks/{replicate}_cutoff_analysis.pdf", replicate = REPLICATES),
        # clean peak 结果
        expand("clean_peaks/cutoff/{replicate}_peaks.{PEAK_TYPE}Peak", replicate = REPLICATES, PEAK_TYPE = PEAK_TYPE),
	# 通过 intersect or idr 进行 peak 筛选
        expand("clean_peaks/{m}/{sample}_peaks.{PEAK_TYPE}Peak", sample=SAMPLE_TO_REPLICATE.keys(), m = PEAK_SELECTION, PEAK_TYPE = PEAK_TYPE),
        # 所有样本共识peaks
        "clean_peaks/merge/merged_peaks.bed" if len(SAMPLE_TO_REPLICATE) > 2 else [],
        #####################################
        # Motif 分析
        #####################################
        expand("motif_analysis/{sample}_summit.fa", sample = SAMPLE_TO_REPLICATE.keys()),
        expand("motif_analysis/{sample}/combined.meme", sample = SAMPLE_TO_REPLICATE.keys()) if config["motif"]["do"] else [],
        #####################################
        # Peak 注释
        #####################################
        expand("peak_annotation/{sample}_peaks_allhits.txt", sample = SAMPLE_TO_REPLICATE.keys()) if config["uropa"]["do"] else [],
        expand("peak_annotation/{sample}_peaks_finalhits.txt", sample = SAMPLE_TO_REPLICATE.keys()) if config["uropa"]["do"] else [],
        #####################################
        # 定量分析
        #####################################
        "counts/merged_peaks.counts.matrix",
        "counts/merged_peaks.TMM.CPM.matrix",
	# 差异分析
	expand("diff_peaks/{contrast}.{m}.DE_results", contrast=config["contrasts"], m=config["diff_peaks"]["method"]) if config["diff_peaks"]["do"] and config["contrasts"] else [],
        expand("diff_peaks_annotation/{contrast}.bed6", contrast=config["contrasts"]) if config["diff_peaks"]["do"] and config["contrasts"] and config["uropa"]["do"] else [],
	#####################################
	# 质控结果 
	#####################################
        # 测序数据质控表格
        "quality_control/fastp_summary.tsv",
        # 比对质控表格
        "quality_control/estimate_read_filtering.tsv",
        # cross correlation 质控表格
        "quality_control/cross_correlation_summary.tsv" if config["cross_correlation"]["do"] else [],

##########################################################
# 使用fastp进行原始数据质控和过滤，自动判断 SE？PE？
# raw_data => clean_data
##########################################################
rule fastp_quality_control:
    input:
        fastq=["raw_data/{replicate}_R1.fastq.gz", "raw_data/{replicate}_R2.fastq.gz"] if SEQ_TYPE == 'PE' else ["raw_data/{replicate}_R1.fastq.gz"]
    output:
        fastq=["clean_data/{replicate}_R1.fastq.gz", "clean_data/{replicate}_R2.fastq.gz"] if SEQ_TYPE == 'PE' else ["clean_data/{replicate}_R1.fastq.gz"],
        html_report="clean_data/{replicate}_fastp.html",
        json_report="clean_data/{replicate}_fastp.json"
    log: "logs/{replicate}_fastp_quality_control.log"
    threads: 3
    singularity:
        PEAKSNAKE_HOME + "/sifs/commonTools_20231218.sif"
    params:
        fastq="-i raw_data/{replicate}_R1.fastq.gz -o clean_data/{replicate}_R1.fastq.gz -I raw_data/{replicate}_R2.fastq.gz -O clean_data/{replicate}_R2.fastq.gz" if SEQ_TYPE == 'PE' else "-i raw_data/{replicate}_R1.fastq.gz -o clean_data/{replicate}_R1.fastq.gz",
        fastp=config["fastp"]
    shell:
        """
        fastp {params.fastq} --html {output.html_report} --json {output.json_report} --thread {threads} {params.fastp} 1>{log} 2>&1
        """

##########################################################
# 根据基因组构建 bowtie2 index
##########################################################
rule bowtie2_build:
    input:
        genome = GENOME
    output:
        index_prefix = "ref/genome.1.bt2"
    log: "logs/bowtie2_build.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/bowtie2_2.5.2.sif"
    threads: 6
    shell:
        "bowtie2-build --threads {threads} {input.genome} ref/genome 1>{log} 2>&1"

##########################################################
# 使用 bowtie2 将测序数据比对到参考基因组
# fastq => sam
##########################################################
rule bowtie2_align:
    input:
        fastq=["clean_data/{replicate}_R1.fastq.gz", "clean_data/{replicate}_R2.fastq.gz"] if SEQ_TYPE == 'PE' else ["clean_data/{replicate}_R1.fastq.gz"],
        genome_index=config["bowtie2_index"] + ".1.bt2" if config["bowtie2_index"] else "ref/genome.1.bt2"
    output:
        sam="raw_bams/{replicate}.sam"
    log: "logs/{replicate}_bowtie2_align.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/bowtie2_2.5.2.sif"
    threads: 4
    params:
        genome_index=config["bowtie2_index"] if config["bowtie2_index"] else "ref/genome",
        fastq="-1 clean_data/{replicate}_R1.fastq.gz -2 clean_data/{replicate}_R2.fastq.gz" if SEQ_TYPE == 'PE' else "-U clean_data/{replicate}_R1.fastq.gz",
        bowtie2=config["bowtie2"] if config["bowtie2"] else ""
    shell:
        """
        bowtie2 -p {threads} -x {params.genome_index} {params.fastq} -S {output.sam} {params.bowtie2} 1>{log} 2>&1
        """

rule sort_bam:
    input:
        sam="raw_bams/{replicate}.sam"
    output:
        sorted_bam="raw_bams/{replicate}_sorted.bam"
    log: "logs/{replicate}_sort_bam.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/commonTools_20231218.sif"
    threads: 4
    shell:
        """
        samtools sort -@ {threads} -o {output.sorted_bam} {input.sam} 1>{log} 2>&1
        samtools index {output.sorted_bam}
        """

rule sieve_alignment:
    input:
        bam="raw_bams/{replicate}_sorted.bam"
    output:
        bam="clean_bams/{replicate}_final.bam"
    log: "logs/{replicate}_sieve_alignment.log"
    threads: 4
    singularity:
        PEAKSNAKE_HOME + "/sifs/deeptools_20231220.sif"
    params:
        peaksnake_home=PEAKSNAKE_HOME,
        minMappingQuality=config["alignmentSieve"]["minMappingQuality"],
        blacklist="--blackListFileName " + config["alignmentSieve"]["blacklist"] if config["alignmentSieve"]["blacklist"] else [],
        extra=config["alignmentSieve"]["extra"] if config["alignmentSieve"]["extra"] else "" 
    shell:
        """
        alignmentSieve --numberOfProcessors {threads} --bam {input.bam} --outFile {output.bam} --filterMetrics {log} --ignoreDuplicates --minMappingQuality {params.minMappingQuality} --samFlagExclude 260 {params.blacklist} {params.extra} 1>{log} 2>&1
        
	samtools index {output.bam}
        """

rule estimate_read_filtering:
    input:
        bams=expand("raw_bams/{replicate}_sorted.bam", replicate=REPLICATES + INPUTS)
    output:
        stat="quality_control/estimate_read_filtering.tsv"
    threads: 4
    singularity:
        PEAKSNAKE_HOME + "/sifs/deeptools_20231220.sif"
    log: "logs/estimate_read_filtering.log"
    params:
        peaksnake_home=PEAKSNAKE_HOME,
        minMappingQuality=config["alignmentSieve"]["minMappingQuality"],
        blacklist="--blackListFileName " + config["alignmentSieve"]["blacklist"] if config["alignmentSieve"]["blacklist"] else "",
        extra=config["alignmentSieve"]["extra"] if config["alignmentSieve"]["extra"] else "",
        sampleLabels=REPLICATES + INPUTS 
    shell:
        """
        estimateReadFiltering \
        --numberOfProcessors {threads} \
	--bam {input.bams} \
        --sampleLabels {params.sampleLabels} \
        --outFile {output.stat} \
	--ignoreDuplicates \
	--minMappingQuality {params.minMappingQuality} \
	--samFlagExclude 260 \
	--blackListFileName ref/blacklist.bed \
        {params.extra} 1>{log} 2>&1
        """

##########################################################
# DeepTools 绘图 
##########################################################
rule convert_bam_to_bigwig:
    input:
        bam="clean_bams/{replicate}_final.bam"
    output:
        bw="clean_bams/{replicate}.bw"
    log: "logs/{replicate}_convert_bam_to_bigwig.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/deeptools_20231220.sif"
    threads: 2
    params:
        gsize=config["gsize"],
	bamCoverage = config["bamCoverage"] if config["bamCoverage"] else ""
    shell:
        """
        bamCoverage -p {threads} --bam {input.bam} -o {output.bw} --effectiveGenomeSize {params.gsize} {params.bamCoverage} 1>{log} 2>&1
	"""

rule summarize_multiple_bigwigs:
    input:
        bws=expand("clean_bams/{replicate}.bw", replicate=REPLICATES + INPUTS),
	tss_tes_bed=config["tss_tes_bed"]
    output:
        "clean_bams/bw_summary.gz"
    params:
        labels=REPLICATES + INPUTS
    log: "logs/summarize_multiple_bigwigs.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/deeptools_20231220.sif"
    threads: 10
    shell:
        """
        multiBigwigSummary BED-file \
        	--bwfiles {input.bws} \
        	--labels {params.labels} \
        	--BED {input.tss_tes_bed} \
        	-o {output} -p {threads} 1>{log} 2>&1 
        """

rule generate_correlation_plots:
    input:
        "clean_bams/bw_summary.gz"
    output:
        pdf="deeptools/sample_correlation.pdf",
        tab="deeptools/sample_correlation.tab"
    log: "logs/generate_correlation_plots.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/deeptools_20231220.sif"
    shell:
        """
        plotCorrelation -in {input} -o {output.pdf} \
            --corMethod pearson --whatToPlot heatmap \
            -min 0.5 \
            --plotTitle "Pearson Correlation of Samples" \
            --outFileCorMatrix {output.tab} 1>{log} 2>&1 
        """

rule plot_heatmap_reference_point:
    input:
        bws=expand("clean_bams/{replicate}.bw", replicate=REPLICATES + INPUTS),
        tss_tes_bed=config["tss_tes_bed"],
        tss_tes_shuffle_bed=config["tss_tes_shuffle_bed"]
    output:
        tss_matrix="deeptools/tss_matrix.gz",
        tss_heatmap="deeptools/tss_heatmap.pdf"
    params:
        labels=REPLICATES + INPUTS
    log: "logs/plot_heatmap_reference_point.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/deeptools_20231220.sif"
    threads: 10
    shell:
        """
        computeMatrix reference-point \
        -S {input.bws} \
        --samplesLabel {params.labels} \
        -R {input.tss_tes_bed} {input.tss_tes_shuffle_bed} \
        --referencePoint TSS \
        -b 5000 -a 5000 \
        --binSize 50 \
        -o {output.tss_matrix} \
        -p {threads} 1>{log} 2>&1
 
        plotHeatmap -m {output.tss_matrix} -o {output.tss_heatmap} --missingDataColor 0.5 1>>{log} 2>&1
        """

rule plot_heatmap_scale_regions:
    input:
        bws=expand("clean_bams/{replicate}.bw", replicate=REPLICATES + INPUTS),
        tss_tes_bed=config["tss_tes_bed"],
        tss_tes_shuffle_bed=config["tss_tes_shuffle_bed"]
    output:
        tss_tes_matrix="deeptools/tss_tes_matrix.gz",
        tss_tes_heatmap="deeptools/tss_tes_heatmap.pdf"
    params:
        labels=REPLICATES + INPUTS
    log: "logs/plot_heatmap_scale_regions.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/deeptools_20231220.sif"
    threads: 10
    shell:
        """
        computeMatrix scale-regions \
        -S {input.bws} \
        --samplesLabel {params.labels} \
        -R {input.tss_tes_bed} {input.tss_tes_shuffle_bed} \
        --regionBodyLength 4000 \
        -b 2000 -a 2000 \
        --binSize 50 \
        -o {output.tss_tes_matrix} \
        -p {threads} 1>{log} 2>&1

        plotHeatmap -m {output.tss_tes_matrix} -o {output.tss_tes_heatmap} --missingDataColor 0.5 1>>{log} 2>&1
        """

##########################################################
# 对每个 replicate:input call peak
##########################################################
# 规则：MACS3 call peak
rule callpeak_with_macs3:
    input:
        sorted_ip_bam="clean_bams/{replicate}_final.bam",
        sorted_input_bam=lambda wildcards: f"clean_bams/{config['samples'][wildcards.replicate]}_final.bam" if config['samples'][wildcards.replicate] else []
    output:
        Peak="raw_peaks/{replicate}_peaks." + PEAK_TYPE + "Peak",
        cutoff_analysis_txt="raw_peaks/{replicate}_cutoff_analysis.txt"
    log: "logs/{replicate}_callpeak_with_macs3.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/macs3_idr_20231218.sif"
    threads: 1
    params:
        control=lambda wildcards: f"-c clean_bams/{config['samples'][wildcards.replicate]}_final.bam" if config['samples'][wildcards.replicate] else "",
        format="BAMPE" if SEQ_TYPE == 'PE' else "BAM",
        gsize=config["gsize"],
        PEAK_TYPE="--broad" if PEAK_TYPE == "broad" else "",
        extra = config["macs3"]["extra"] if config["macs3"]["extra"] else ""
    shell:
        """
        macs3 callpeak -g {params.gsize} -t {input.sorted_ip_bam} {params.control} --name raw_peaks/{wildcards.replicate} --format {params.format} --keep-dup all --qvalue 0.075 --cutoff-analysis {params.PEAK_TYPE} {params.extra} 1>{log} 2>&1
        """

rule plot_macs_cutoff_analysis:
    input:
        cutoff_analysis_txt="raw_peaks/{replicate}_cutoff_analysis.txt"
    output:
        cutoff_analysis_pdf="raw_peaks/{replicate}_cutoff_analysis.pdf"
    log: "logs/{replicate}_plot_macs_cutoff_analysis.log"
    shell:
        """
        python {PEAKSNAKE_HOME}/scripts/plot_macs_cutoff_analysis.py {input.cutoff_analysis_txt} {output} 1>{log} 2>&1
        """

rule filter_peaks_by_qscore:
    input:
        Peak="raw_peaks/{replicate}_peaks." + PEAK_TYPE + "Peak"
    output:
        Peak="clean_peaks/cutoff/{replicate}_peaks." + PEAK_TYPE + "Peak"
    params:
        qscore=config["macs3"]["qscore"]
    shell:
        """
        awk '$9>{params.qscore}' {input.Peak} > {output.Peak}
        """

rule select_peaks_norep:
    input:
        Peak="clean_peaks/cutoff/{sample}_rep1_peaks." + PEAK_TYPE + "Peak"
    output:
        Peak="clean_peaks/norep/{sample}_peaks." + PEAK_TYPE + "Peak"
    shell:
        """
        cp {input.Peak} {output.Peak} 
        """ 

rule select_peaks_by_intersect:
    input:
        Peak=lambda wildcards: expand("clean_peaks/cutoff/" + wildcards.sample + "_{rep}_peaks." + PEAK_TYPE + "Peak", rep=SAMPLE_TO_REPLICATE[wildcards.sample])
    output:
        Peak="clean_peaks/intersect/{sample}_peaks." + PEAK_TYPE + "Peak"
    params:
        min_overlap=config['intersect']['min_overlap']
    shell:
        """
        # 检查输入文件的数量
        num_peaks=$(echo {input.Peak} | wc -w)

        # 如果只有一个输入文件
        if [ "$num_peaks" -eq 1 ]; then
            cp {input.Peak[0]} {output.Peak}
        else
            # 复制第一个输入文件到临时文件
            cp {input.Peak[0]} {wildcards.sample}.temp.bed

            # 使用除第一个之外的所有输入文件
            echo {input.Peak} | tr ' ' '\\n' | awk 'NR>1' | while read bed; do
                bedtools intersect -f {params.min_overlap} -r -a {wildcards.sample}.temp.bed -b $bed -wa > {wildcards.sample}.temp2.bed
                mv {wildcards.sample}.temp2.bed {wildcards.sample}.temp.bed
            done

            # 创建一个中间的 peak list 文件
            cut -f 4 {wildcards.sample}.temp.bed > {wildcards.sample}.peak_lst

            # 使用中间的 peak list 文件和第一个输入文件生成最终输出
            awk 'NR==FNR {{a[$1]; next}} $4 in a' {wildcards.sample}.peak_lst {input.Peak[0]} > {output.Peak}

            # 清理临时文件
            rm {wildcards.sample}.temp.bed {wildcards.sample}.peak_lst
        fi
        """

rule select_peaks_by_idr:
    input:
        rep1_peaks="raw_peaks/{sample}_rep1_peaks." + PEAK_TYPE + "Peak",
        rep2_peaks="raw_peaks/{sample}_rep2_peaks." + PEAK_TYPE + "Peak"
    output:
        true_rep_idr="clean_peaks/idr/{sample}_true_rep_idr.txt",
        idr_peaks="clean_peaks/idr/{sample}_peaks." + PEAK_TYPE + "Peak"
    log: "logs/{sample}_select_peaks_by_idr.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/macs3_idr_20231218.sif"
    threads: 1
    params:
        PEAK_TYPE=PEAK_TYPE,
        idr_threshold=config["idr"]["idr_threshold"]
    shell:
        """
        idr --samples {input.rep1_peaks} {input.rep2_peaks} --idr-threshold {params.idr_threshold} --output-file {output.true_rep_idr} --plot --input-file-type {PEAK_TYPE}Peak --rank p.value 1>{log} 2>&1 

        awk -v OFS="\\t" 'BEGIN {{FS=OFS}} {{ $4=$1":"$2"_"$3; print $1, $2, $3, $4, $5, $6, $7, $8, $9, $10 }}' {output.true_rep_idr} | sort -k1,1 -k2,2n -k3,3n > {output.idr_peaks}
        """

##########################################################
# Motif 分析
##########################################################
rule extract_peak_summit_fasta:
    input:
        Peak="clean_peaks/" + PEAK_SELECTION + "/{sample}_peaks." + PEAK_TYPE + "Peak"
    output:
        summit_fa="motif_analysis/{sample}_summit.fa"
    params:
        top_n=config["motif"]["top_n"],
        summit_flank=config["motif"]["summit_flank"],
        genome=config["genome"]
    shell:
        """
        set +o pipefail;
        sort -k8,8nr {input.Peak} | head -n {params.top_n} | awk -v OFS='\\t' '{{print $1,$2+$10-{params.summit_flank},$2+$10+{params.summit_flank} + 1}}' | awk '$2>=0' | bedtools getfasta -fi {params.genome} -bed - > {output.summit_fa}
        """

rule motif_discovery:
    input:
        summit_fa="motif_analysis/{sample}_summit.fa"
    output:
        "motif_analysis/{sample}/combined.meme"
    log: "logs/{sample}_motif_discovery.log"
    params:
        motif_databases=config['motif']['motif_databases'],
        outdir="motif_analysis/{sample}",
        extra=config['motif']['extra'] if config['motif']['extra'] else ""
    singularity:
        PEAKSNAKE_HOME + "/sifs/memesuite_latest.sif"
    threads: 4
    shell:
        """
        meme-chip -meme-p {threads} -db {params.motif_databases} -oc {params.outdir} {params.extra} {input.summit_fa} 1>{log} 2>&1
        """

##########################################################
# Peak 注释
##########################################################
rule peak_annotation_with_uropa:
    input:
        Peak="clean_peaks/" + PEAK_SELECTION + "/{sample}_peaks." + PEAK_TYPE + "Peak",
        gtf=config["gtf"]
    output:
        allhits="peak_annotation/{sample}_peaks_allhits.txt",
        finalhits="peak_annotation/{sample}_peaks_finalhits.txt"
    log: "logs/{sample}_peak_annotation_with_uropa.log"
    params:
        feature_anchor=config["uropa"]["feature_anchor"],
        distance=config["uropa"]["distance"],
        relative_location=config["uropa"]["relative_location"]
    singularity:
        PEAKSNAKE_HOME + "/sifs/uropa_4.0.3--pyhdfd78af_0.sif"
    shell:
        """
        uropa --bed {input.Peak} --gtf {input.gtf} --feature gene --feature-anchor {params.feature_anchor} --distance {params.distance} --relative-location {params.relative_location} --outdir peak_annotation 1>{log} 2>&1 
        """

##########################################################
# 生成所有 samples 共识 peaks
##########################################################
rule merge_peaks:
    input:
        sample_peaks=expand("clean_peaks/" + PEAK_SELECTION + "/{sample}_peaks." + PEAK_TYPE + "Peak", sample=SAMPLE_TO_REPLICATE.keys())
    output:
        merged_peaks_bed="clean_peaks/merge/merged_peaks.bed",
        merged_peaks_saf="clean_peaks/merge/merged_peaks.saf"
    singularity:
        PEAKSNAKE_HOME + "/sifs/commonTools_20231218.sif"
    params:
        fai=config['genome'] + ".fai"
    shell:
        """
        mkdir -p clean_peaks/merge
        cat {input.sample_peaks} > clean_peaks/merge/cat_peaks.bed
        bedtools sort -i clean_peaks/merge/cat_peaks.bed -g {params.fai} > clean_peaks/merge/cat_sorted_peaks.bed
        bedtools merge -i clean_peaks/merge/cat_sorted_peaks.bed > {output.merged_peaks_bed}
        awk 'OFS="\t" {{print $1":"$2+1"-"$3, $1, $2+1, $3, "."}}' {output.merged_peaks_bed} > {output.merged_peaks_saf}
        """

##########################################################
# 使用 feature counts 计算 replicate peak counts
##########################################################
rule run_feature_counts:
    input:
        bam="clean_bams/{replicate}_final.bam",
        merged_peaks_saf="clean_peaks/merge/merged_peaks.saf"
    output:
        counts="counts/{replicate}.count",
        stat="counts/{replicate}.log"
    log: "logs/{replicate}_run_feature_counts.log"
    params:
        peaksnake_home=PEAKSNAKE_HOME,
        isPairedEnd="TRUE" if SEQ_TYPE == 'PE' else "FALSE"
    shell:
        """
        Rscript {params.peaksnake_home}/software/RunFeatureCounts/run-featurecounts.R -b {input.bam} --saf {input.merged_peaks_saf} --isPairedEnd {params.isPairedEnd} -o counts/{wildcards.replicate} 1>{log} 2>&1
        """

##########################################################
# 合并生成 replicate counts 矩阵
##########################################################
rule create_count_matrix:
    input:
        expand("counts/{replicate}.count", replicate=REPLICATES)
    output:
        counts_matrix="counts/merged_peaks.counts.matrix",
        cpm_matrix="counts/merged_peaks.TMM.CPM.matrix"
    log: "logs/create_count_matrix.log"
    params:
        peaksnake_home=PEAKSNAKE_HOME
    shell:
        """
        ls {input} >counts/count.fofn
        perl {params.peaksnake_home}/software/RunFeatureCounts/abundance_estimates_to_matrix.pl --est_method featureCounts --quant_files counts/count.fofn --out_prefix counts/merged_peaks 1>{log} 2>&1
        """

##########################################################
# 使用 DESeq2/ edgeR 进行差异分析
##########################################################

if config["contrasts"]:
    # 生成 samples.txt
    with open('samples.txt', 'w') as file:
        for ip in REPLICATES:
            # 提取 sample name
            sample_name = '_'.join(ip.split('_')[:2])
            file.write(f"{sample_name}\t{ip}\n")

    # 生成 contrasts.txt
    with open("contrasts.txt", "w") as file:
        file.write("\n".join([" ".join(item.split("_vs_")) for item in config["contrasts"]]))

rule run_deseq2:
    input:
        "counts/merged_peaks.counts.matrix"
    output:
        expand("diff_peaks/{contrast}.DESeq2.DE_results", contrast=config["contrasts"])    
    log: "logs/run_deseq2.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/trinity_20231218.sif"
    shell:
        """
        run_DE_analysis.pl -m {input} --method DESeq2 -s samples.txt --contrasts contrasts.txt -o diff_peaks 1>{log} 2>&1

        cd diff_peaks/
        rm *count_matrix *.MA_n_Volcano.pdf *.Rscript
        for file in merged_peaks.counts.matrix.*.DE_results; do
            echo -e "PeakID\tsampleA\tsampleB\tFoldChange\tPValue\tPadj" >"${{file#merged_peaks.counts.matrix.}}"
            grep -v "^sampleA" $file | awk 'BEGIN {{OFS="\t"}} {{ $7 = exp(log(2) * $7); print $1,$2,$3,$7,$10,$11}}' >> "${{file#merged_peaks.counts.matrix.}}"
            rm $file
        done
        cd ..
        """

rule run_edgeR:
    input:
        "counts/merged_peaks.counts.matrix"
    output:
        expand("diff_peaks/{contrast}.edgeR.DE_results", contrast=config["contrasts"])
    log: "logs/run_edgeR.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/trinity_20231218.sif"
    shell:
        """
        run_DE_analysis.pl -m {input} --method edgeR -s samples.txt --contrasts contrasts.txt -o diff_peaks 1>{log} 2>&1

        cd diff_peaks/
        rm *count_matrix *.MA_n_Volcano.pdf *.Rscript
        for file in merged_peaks.counts.matrix.*.DE_results; do
            echo -e "PeakID\tsampleA\tsampleB\tFoldChange\tPValue\tPadj" >"${{file#merged_peaks.counts.matrix.}}"
            grep -v "^sampleA" $file | awk 'BEGIN {{OFS="\t"}} {{ $4 = exp(log(2) * $4); print $1,$2,$3,$4,$6,$7}}' >> "${{file#merged_peaks.counts.matrix.}}"
            rm $file 
        done
        cd .. 
        """

rule diff_peaks_annotation_with_uropa:
    input:
        diff_peaks="diff_peaks/{contrast}.edgeR.DE_results",
        gtf=config["gtf"]
    output:
        diff_peaks_bed="diff_peaks_annotation/{contrast}.bed6",
        allhits="diff_peaks_annotation/{contrast}_allhits.txt",
        finalhits="diff_peaks_annotation/{contrast}_finalhits.txt"
    log: "logs/{contrast}_diff_peaks_annotation_with_uropa.log"
    params:
        diff_peaks_padj=config["diff_peaks"]["padj"],
        feature_anchor=config["uropa"]["feature_anchor"],
        distance=config["uropa"]["distance"],
        relative_location=config["uropa"]["relative_location"]
    singularity:
        PEAKSNAKE_HOME + "/sifs/uropa_4.0.3--pyhdfd78af_0.sif"
    shell:
        """
        awk 'BEGIN {{FS="\\t"; OFS="\t"}} NR>1 && $6 < {params.diff_peaks_padj} {{split($1, arr, "[:-]"); print arr[1], arr[2]-1, arr[3], $1, $4, "."}}' {input.diff_peaks} > {output.diff_peaks_bed}

        uropa --bed {output.diff_peaks_bed} --gtf {input.gtf} --feature gene --feature-anchor {params.feature_anchor} --distance {params.distance} --relative-location {params.relative_location} --outdir diff_peaks_annotation 1>{log} 2>&1
        """

##########################################################
# 合并fastp质控结果生成表格
##########################################################
rule combine_fastp_reports:
    input:
        expand("clean_data/{replicate}_fastp.json", replicate=REPLICATES + INPUTS)
    output:
        "quality_control/fastp_summary.tsv"
    log: "logs/combine_fastp_reports.log"
    params:
        peaksnake_home=PEAKSNAKE_HOME
    shell:
        """
        Rscript {params.peaksnake_home}/scripts/combine_fastp_report.R --input {input} --output quality_control/ 1>{log} 2>&1
        """

##########################################################
# cross correlation
##########################################################
rule cross_correlation:
    input:
        bam="clean_bams/{replicate}_final.bam"
    output:
        pdf="quality_control/cross_correlation/{replicate}.pdf",
        tsv="quality_control/cross_correlation/{replicate}.tsv"
    log: "logs/{replicate}_cross_correlation.log"
    singularity:
        PEAKSNAKE_HOME + "/sifs/phantompeakqualtools_20231218.sif"
    params:
        spp=config['cross_correlation']['spp'] if config['cross_correlation']['spp'] else ""
    threads: 4
    shell:
        """
        run_spp.R -p={threads} -c={input.bam} -savp={output.pdf} -out={output.tsv} -rf {params.spp} 1>{log} 2>&1 
        """

rule cross_correlation_summary:
    input:
        expand("quality_control/cross_correlation/{replicate}.tsv", replicate=REPLICATES + INPUTS)
    output:
        "quality_control/cross_correlation_summary.tsv"
    shell:
        """ 
        echo -e "Sample\\tTotalReadsFiltered\\tFragmentLength\\tCrossCorrelation\\tPhantomPeakLocation\\tPhantomPeakCorrelation\\tMinimumCrossCorrelationShift\\tMinimumCrossCorrelationValue\\tNSC\\tRSC\\tPhantomPeakQualityTag" >{output}
	cat {input} | sort -k 1 >>{output}
        """