Script Flowchart - genetics-of-dna-methylation-consortium/goDMC_phase2 GitHub Wiki

flowchart TB
    %%{
  init: {
    'themeVariables': {
      'lineColor': '#738290'
            }
        }
    }%%

    %%Class style%%
    classDef ready-green fill:#6eeb83,stroke:#220901,stroke-width:2px,font-size:18px,color:#000
    classDef developing-yellow fill:#e4ff1a,stroke:#220901,stroke-width:2px,font-size:18px,color:#000
    classDef notready-red fill:#ff5714,stroke:#220901,stroke-width:2px,font-size:18px,color:#000
    classDef process-white fill:#edf2f4,stroke:#edf2f4,font-size:20px,color:#000
    classDef qtl-pink fill:#ffe9f3,stroke:#ffe9f3,stroke-width:4px,font-size:20px,color:#000
    classDef was-orange fill:#fed9b7,stroke:#fed9b7,stroke-width:4px,font-size:20px,color:#000

    %%sub modules%%
    subgraph setup["install and setup"]
        direction TB
        gitclone("git clone and git pull")
        config("modify config file")
        sftp("set the SFTP details")
        inputdata("prepare input dataset")
    end

    subgraph preprocessing["process SNP data and methylation data"]
        direction TB
        01("01-check_data.sh")
        00("00-setup_folders.sh")
        02a("02a-snp_data.sh")
        02b("02b-convert_snp_format.sh")
        03a("03a-methylation_variables.sh")
    end
    subgraph processMethB["process methylation data"]
        direction TB
        03b("03b-methylation_adjustment1.sh ${meth_chunks}")
        03b_aggregate("submission_scripts_template/godmc_03b_aggregate.sh")
        03c("03c-methylation_pcs.sh")
        03d("03d-non_genetic_methylation_pcs.sh")
    end
    subgraph processMethC["process methylation data"]
        direction TB
        03e("03e-methylation_adjustment2.sh ${meth_chunks}")
        aggregate_adj2("./resources/methylation/aggregate_adjustment2.sh")
        03f("03f-convert_methylation_format.sh")
        03g("03g-perform_positive_control.sh")
    end
    subgraph mQTL["mQTL analysis"]
        direction TB
        04a("04a-convert_snp_format.sh")
        04b("04b-mapper-preparation.sh")
        04c("04c-create_mapper_files.sh")
        04d("04d-encoding.sh")
        04e("04e-single-site-analysis.sh")
        04f("04f-tar_results.sh")
    end
    subgraph varianceQTLs["variance meQTLs analysis"]
        direction TB
        07a("07a-vmeQTL_data_preparation.sh")
        07b("07b-run_cis_vmeQTL.sh")
        07c("07c-run_cis_vmeQTL.sh")
        07d("07d-tar_results.sh")
    end
    subgraph inversionQTLs["inversion mQTLs analysis"]
        direction TB
        08b("08b-inversionmeQTL.sh")
        08a("08a-genotypeInversion.sh")
        08c("08c-IWAS_phenotype.sh phenotype")
        08d("08d-mediation_inversion_CpG_phenotype.sh phenotype")
    end
    subgraph PRS_EWAS["PRS_EWAS"]
        09("09-PRS_EWAS.sh")
    end
    subgraph ageaccGWAS["GWAS of age acceleration"]
        direction TB
        10b("10b-hertability_aar.sh")
        10a("10a-gwas_aar.sh")
    end
    subgraph epismokingGWAS["GWAS of smoking"]
        direction TB
        11b("11b-heritability_smoking.sh")
        11a("11a-gwas_smoking.sh")
        11c("11c-check_compress_data.sh")
    end
    subgraph nc886GWAS["GWAS of the imprinted gene nc886"]
        14("14-nc886_gwas.sh")
    end
    subgraph status["status"]
        direction TB
        ready("scripts ready to be run")
        dev("scripts under development")
        notready("scripts not ready to be run")
    end

    %%relationships%%
    gitclone --> config
    config -->  sftp
    sftp --> inputdata
    00 --> 01
    01 --> 02a
    02a --> 02b
    02b --> 03a
    03b --> 03b_aggregate
    03b_aggregate --> 03c
    03c --> 03d
    03e --> aggregate_adj2
    aggregate_adj2 --> 03f
    03f --> 03g
    04a --> 04b
    04b --> 04c
    04c --> 04d
    04d --> 04e
    04e --> 04f
    07a --> 07b
    07b --> 07c
    07c --> 07d
    10a --> 10b
    11a --> 11b
    11b --> 11c
    08a --> 08b
    08b --> 08c
    08c --> 08d
    notready --> dev
    dev --> ready
    setup --> preprocessing
    preprocessing -- <font size="5px">check_upload.sh 03a </font> --> processMethB & nc886GWAS & ageaccGWAS
    processMethB -- <font size="5px">check_upload.sh 03d </font> --> processMethC & PRS_EWAS
    processMethC -- <font size="5px">check_upload.sh 03 </font> --> mQTL & inversionQTLs
    mQTL -- <font size="5px">check_upload.sh</font> --> varianceQTLs
    ageaccGWAS --> epismokingGWAS
    epismokingGWAS --> googledrive("<font size="5px">Google Drive</font>")
    inversionQTLs --> check_upload2("<font size="5px">check_upload.sh</font>")
    varianceQTLs --> check_upload3("<font size="5px">check_upload.sh</font>")
    PRS_EWAS --> check_upload4("<font size="5px">check_upload.sh</font>")
    nc886GWAS --> check_upload5("<font size="5px">check_upload.sh</font>")

    %%assign the style%%
    14:::ready-green
    01:::ready-green
    00:::ready-green
    02a:::ready-green
    02b:::ready-green
    03a:::ready-green
    03c:::ready-green
    03b:::ready-green
    03d:::ready-green
    03b_aggregate:::ready-green
    09:::ready-green
    03f:::ready-green
    03e:::ready-green
    aggregate_adj2:::ready-green
    03g:::ready-green
    04a:::ready-green
    04b:::ready-green
    04c:::ready-green
    04d:::ready-green
    04e:::ready-green
    04f:::ready-green
    07b:::ready-green
    07a:::ready-green
    07c:::ready-green
    07d:::ready-green
    10b:::ready-green
    10a:::ready-green
    11b:::ready-green
    11a:::ready-green
    11c:::ready-green
    08b:::ready-green
    08a:::ready-green
    08c:::developing-yellow
    08d:::developing-yellow
    gitclone:::ready-green
    config:::ready-green
    sftp:::ready-green
    inputdata:::ready-green
    ready:::ready-green
    dev:::developing-yellow
    notready:::notready-red
    check_upload2:::ready-green
    check_upload3:::ready-green
    check_upload4:::ready-green
    check_upload5:::ready-green

    setup:::process-white
    preprocessing:::process-white
    processMethB:::process-white
    ageaccGWAS:::was-orange
    epismokingGWAS:::was-orange
    PRS_EWAS:::was-orange
    nc886GWAS:::was-orange
    processMethC:::process-white
    mQTL:::qtl-pink
    inversionQTLs:::qtl-pink
    varianceQTLs:::qtl-pink
    status:::process-white