flowchart TD;
classDef default stroke-width: 2px ;
classDef qc fill: #ffffff ;
    A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
    A -->|Trimmomatic| B("Trim (.fastq.gz)")
    B -->|Fastqc| a
    B -->|STAR| C("Map (.bam)")
    C -->|RseQC| c{{"Infer experiment"}}
    C -->|featureCount| D("Count (.txt)")
    D --> E("Downstream analysis")
class a,c qc

flowchart TD;
classDef default stroke-width: 2px ;
classDef qc fill: #ffffff ;
    A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
    A -->|Trimmomatic| B("Trim (.fastq.gz)")
    B -->|Fastqc| a
    B -->|Bowtie2| C("Map (.sam)")
    C -->|Samtools| D("Sort (.bam)")
    D -->|Picard: MarkDuplicates| E("Deduplication (.bam)")
    E -->|Samtools + egrep| F("Filter (.bam)")
    F -->|Picard: CollectInsertSizeMetrics| f{{"Insert size"}}
    F -->|bedtools| G("Shift (.bed)")
    F -->|Samtools: index + deepTools: bamCoverage| J("Track (.bw)")
    subgraph H [Call peak for every sample]
    a1("a rep_1\n(.nPeak)")
    a2("a rep_2\n(.nPeak)")
    an("...")
    b1("b rep_1\n(.nPeak)")
    b2("b rep_2\n(.nPeak)")
    bn("...")
    nn("...")
    end
    subgraph I [Call peak for grouped sample]
        subgraph Ia [a]
        Ia_1("a rep_1")
        Ia_2("a rep_2")
        Ia_n("...")
        an("...")
        end
        Ia --> Ia_res1("(.nPeak)")
        Ia --> Ia_res2("(.bdg)")
        subgraph Ib [b]
        Ib_1("b rep_1")
        Ib_2("b rep_2")
        Ib_n("...")
        an("...")
        end
        Ib --> Ib_res1("(.nPeak)")
        Ib --> Ib_res2("(.bdg)")
        In("...")
    end
    G -->|MACS2| H
    G -->|MACS2| I
    subgraph K [Consensus peakset]
    Ka("a (.nPeak)")
    Kb("b (.nPeak)")
    Kn("...")
    end
    I -->|IDR| K
    H -->|IDR| K
    I -->|bedGraphToBigWig| L("Track (.bw)")
    K --> M("Downstream analysis")
class a,f,Ia,Ib qc

flowchart TD;
classDef default stroke-width: 2px ;
classDef qc fill: #ffffff ;
    A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
    A -->|Trimmomatic| B("Trim (.fastq.gz)")
    B -->|Fastqc| a
    B -->|Bowtie2| C("Map (.sam)")
    C -->|Samtools| D("Sort (.bam)")
    D -->|Picard: MarkDuplicates| E("Deduplication (.bam)")
    E -->|Samtools + egrep| F("Filter (.bam)")
    F -->|Picard: CollectInsertSizeMetrics| f{{"Insert size"}}
    F -->|bedtools| G("Shift (.bed)")
    F -->|Samtools: index + deepTools: bamCoverage| J("Track (.bw)")
    subgraph H [Call peak for every sample]
    Ha_1("rep_1\n(.nPeak)")
    Ha_2("rep_2\n(.nPeak)")
    Ha_n("...")
    end
    subgraph I [Call peak for grouped sample]
        subgraph Ia [group]
        Ia_1("rep_1")
        Ia_2("rep_2")
        Ia_n("...")
        end
        Ia --> Ia_res1("(.nPeak)")
        Ia --> Ia_res2("(.bdg)")

    end
    G -->|MACS2| H
    G -->|MACS2| I
    I -->|IDR| K("Consensus peakset (.nPeak)")
    H -->|IDR| K
    I -->|bedGraphToBigWig| L("Track (.bw)")
    K --> M("Downstream analysis")
class a,f,Ia qc

flowchart TD;
classDef default stroke-width: 2px ;
classDef qc fill: #ffffff ;
    A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
    A -->|Trimmomatic| B("Trim (.fastq.gz)")
    B -->|Fastqc| a
    B -->|Bowtie2| C("Map (.sam)")
    C -->|Samtools| D("Sort (.bam)")
    D -->|Picard: MarkDuplicates| E("Deduplication (.bam)")
    E -->|Samtools + egrep| F("Filter (.bam)")
    F -->|deepTools: plotFingerprint| f{{"Coverage"}}
    F -->|MACS2| G("Call peak (.bPeak)")
    F -->|Samtools: index + deepTools: bamCompare| H("Track (.bw)")
    G --> I("Downstream analysis") 
class a,f qc

flowchart TD;
classDef default stroke-width: 2px ;
classDef qc fill: #ffffff ;
    A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
    A -->|Bismark| B("Map (.bam)")
    B -->|Bismark: deduplicate_bismark| C("Deduplication (.bam)")
    C -->|Bismark: bismark_methylation_extractor| D("Report CG (.txt)")
    subgraph E [lambda]
    E1("Map (.bam)") --> E2("Deduplication (.bam)") --> E3("Report CG (.txt)")
    end
    A -->|Bismark| E
    E --> F("Filter (.txt)")
    D --> F
    F -->|awk| G("Arrange (.bdg)")
    G --> H("Downstream analysis")
    G -->|sort + bedGraphToBigWig| I("Track (.bw)")
class a qc