TDAS/tdas_config.json5

{
    //This is the default config file for TRS pipline
    //any params given in "param_name":[true, "param"] will appear as --param_name param in the cmdline
    //or params which are not lists will give to this scripts directly, so don't delete them
    "seq_info_format":[",","project","seq1","seq2","config_id"], 
    //define the format of input seqs here, config_id will be "DEFAULT" as default,and the first one is delimeter, and second term must be project, which is an id
    "DEFAULT":{
        "order":["helloworld","trim","STAR","featureCounts","format","redistribute"],
        /* order to perform functions, can define self here, if need to run some funcions, input like this "featureCounts/1",they will call up same parse functions*/
        "order_multiprojects":["generate_cmd"],
        "cmd_name":"trs.cmd",
        "log_name":"trs.log",
        "outdir":"trsout", 
        //the params in the command line when you run this will overwrite this if provided
        //devide cmd to several parsts, if you has some cmds must excute after some other ones finished. key is the id used below, and value is cmd file suffix
        "cmd_fusion_order":["1"], 
        //how to fusion different parts of cmd, values is the id above
        "workflow":
        {
            "helloworld":
            {
                need:true,
                path:"echo",
                params:{
                    " ":"\" hello world\""
                }
            },

            "trim":
            {
                "need":true, 
                // if turn it to false, the command will not run actually but just give the position of files it should give to below pipline, may cause error!
                "father":{"iseq1":["raw","seq1"],"iseq2":["raw","seq2"]},
                "path":"trim_galore", 
                //path of the sorfware
                "outdir":"trimed",
                "cmd_part":"1",
                "variables":
                {

                },//define varibales you want to use in params, beside this you can use outdir and project, and variables defined in father
                "check_paths":[],
                "params":{
                    "--paired":"",
                    "--length":"20",
                    "--quality":"20",
                    "--fastqc":"",
                    "--fastqc_args":"\"--threads 8 \"",
                    " ":"{iseq1} {iseq2}",
                    "-o":"{outdir}",//可以调整，不应该删除
                },
                "outparams":
                {
                    "example":"{project}/hello",
                    //this example can transfer variables to other modules
                }
            },
            "STAR":
            {
                "need":true,
                "father":{"iseq1":["trim","oseq1"],"iseq2":["trim","oseq2"]},
                //here defines what it should extract info and where it extract from. 
                //Correspondingly, the father should give these attributes to the intermedia
                //the key is used to extract infomation, the first one in list is the source of information
                //if "byhand" ,means get these information provided by other inputs in json format, the first param in list is the filename
                //if  "raw" ,means get these information from seq_info_format table defined by top
                //
                "check_paths":[],
                "path":"STAR",
                "cmd_part":"1",
                "outdir":"star",
                "variables":
                {
                    
                },
                "params":{
                    "--genomeDir":"/mnt/Storage2/home/DB/STAR/hg38",
                    "--runThreadN":"10",
                    "--outSAMattributes":"NH HI NM MD XS AS",
                    "--outFilterMultimapNmax":"500",
                    "--outSAMtype":"BAM SortedByCoordinate",//don't change this
                    "--readFilesCommand":"zcat",
                    "--readFilesIn":"{iseq1}  {iseq2}",
                    "--outFileNamePrefix":"{outdir}/{project}/{project}_",
                    //outdir is a variabbe, will replace by os.path.join(root_outdir,outdir)
                },
                "outparams":
                {
                }

            },
            "featureCounts":
            {
                "need":true,
                "father":{"ibam":["STAR","obam_sorted"]},
                "path":"featureCounts",
                "check_paths":[],
                "cmd_part":"1",
                "outdir":"features",
                "variables":{
                    "outputpath":"{outdir}/{project}"
                },
                "functions":["mkdirs(\"{outputpath}\")"],

                "params":
                {
                    "-g":"gene_id",
                    //metagene option
                    "-O":" ",
                    //allow overlap
                    "--fracOverlap":"0.1",
                    //max overlap fraction
                    "-p":" ",
                    //pair end
                    "-B":" ",
                    "-M":" ",
                    //allow  multi mapping
                    "--fraction":" ", 
                    // if counts fractional if a reads overlap of multimapping
                    "-T":"10", 
                    // threads
                    "-a":"/mnt/Storage2/home/zengshiyang/DB/refGene/hg38.repeats.gtf", 
                    // annoation file
                    "-R":"BAM",
                    //output feature count results in bam format
                    "-o":"{outputpath}/{project}_featurecounts",
                    " ":"{ibam}"
                },
                "outparams":{
                    "obam":"{outputpath}/{project}_Aligned.sortedByCoord.out.bam.featureCounts.bam"
                }

            },
            "format":
            {
                "need":true,
                "father":{ibam:["featureCounts","obam"]},
                "path":"samtools view",
                "check_paths":[],
                "cmd_part":"1",
                "outdir":"features",

                "params":
                {
                    "-@":"10",
                    " ":"-x BX -x NH -x AS -x nM -x HI -x IH -x NM -x uT -x MD -x jM -x jI -x XN -x XS -x XS",
                    "  ":"{ibam}",
                    "| grep -e": "\"XT:Z\"",
                    ">":"{outdir}/{project}/{project}_featurecounts.sam.txt"
                }

            },
            "redistribute":
            {
                "need":true,
                "father":{"isam":["format","osam"]},
                "path":"redistribute_multiple_aligned_reads.r",
                "check_paths":[],
                "cmd_part":"1",
                "outdir":"distribution",
                "variables":
                {
                    "outputpath":"{outdir}/{project}"
                },
                "functions":["mkdirs('{outputpath}')"],
                "params":
                {
                    "-r":"/mnt/Storage2/home/zengshiyang/DB/refGene/hg38.repeats.saf",
                    "-s":"50",
                    "-m":1,
                    "-p":"12",
                    //threads
                    "-n":"{outputpath}/{project}_distribution.txt",
                    "-f":"{isam}"
                }

            }
        },

    }
}