nextflow.config.user

nextflow.enable.dsl = 1

params {

    /****************************************
     Input
     ****************************************/

    INPUT_GENOME       = "[The path to the directory that contains 'sample_data_cel/']/sample_data_cel/GCF_000002985.6_WBcel235_genomic.commentModified.fna"
    INPUT_MASKEDGENOME = "[The path to the directory that contains 'sample_data_cel/']/sample_data_cel/GCF_000002985.6_WBcel235_genomic.commentModified.masked.fna"
    INPUT_REPOUT       = "[The path to the directory that contains 'sample_data_cel/']/sample_data_cel/GCF_000002985.6_WBcel235_genomic.out"
    INPUT_RNASEQR1     = "[The path to the directory that contains 'sample_data_cel/']/sample_data_cel/SRR5849934_1.fastq"
    INPUT_RNASEQR2     = "[The path to the directory that contains 'sample_data_cel/']/sample_data_cel/SRR5849934_2.fastq"
//    RNASEQ_OTHER1      = "/full/path/to?additional RNA-Seq-based method GFF"
//    RNASEQ_OTHER2      = "/full/path/to?additional RNA-Seq-based method GFF"
//    HOMOLOGY_OTHER1    = "/full/path/to?additional homology-based method GFF"
//    HOMOLOGY_OTHER2    = "/full/path/to?additional homology-based method GFF"
//    ABINITIO_OTHER1    = "/full/path/to?additional ab initio-based method GFF"
//    ABINITIO_OTHER2    = "/full/path/to?additional ab initio-based method GFF"
    
    HOMOLOGY_DATA = [
        "PREFIX"  : ["Cbriggsae",   // No.1
                     "Ppacificus"], // No.2
        "PROTEIN" : ["[The path to the directory that contains 'sample_data_cel/']/sample_data_cel/GCF_000004555.2_CB4_translated_cds.faa", // No.1
                     "[The path to the directory that contains 'sample_data_cel/']/sample_data_cel/GCA_000180635.4_El_Paco_v._4_translated_cds.faa"], // No.2
        "SPALNDB" : ["NematodC", // No.1
                     "NematodC"] // No.2
    ]

    AUGUSTUS_SPEC          = "test" // [Augustus]/config/species must not have files with the same name

    /****************************************
     Output
     ****************************************/

    // --- Directory to publish results ---

    PDIR      = "[The path to the output directory (e.g. '/XXX/XXX/output_cel/']"

    /****************************************
     General
     ****************************************/
    
    // --- Scratch dirs ---
    SCRATCH     = "/scratch"
    
    // --- ---
    N_THREAD    = 20
    
    // --- ---
    MAX_MEMORY  = "250G"

    /****************************************
     RNA-Seq mapping based
     ****************************************/

    // --- Tools for to_merge ---
    MIN0        = 90 // MINはtranscriptの最小base長

    MIN1        = 300 // MINはtranscriptの最小base長
    
    /****************************************
     RNA-Seq denovo based
     ****************************************/

    // --- Tools for trinity ---
    SRA_FLAG        = 1

    /****************************************
     Ab initio based
     ****************************************/

    AUGUSTUS_TRAINING_SIZE = 1000 // `echo 1000`
    SNAP_TRAINING_SIZE  = AUGUSTUS_TRAINING_SIZE
    AUGUSTUS_TRAINING_DATA = "${PDIR}/Prep/mapping/to_learn_2nd/ginger_learn_2nd.gff3" // gff
    SNAP_TRAINING_DATA  = "${PDIR}/Prep/mapping/to_learn_2nd/ginger_learn_2nd.gff3" // gff_p

    /****************************************
     Merge phase; step1
     ****************************************/
    MAPPING_WEIGHT  = 1.6
    DENOVO_WEIGHT   = 1.4
    HOMOLOGY_WEIGHT = 2.0
    AUGUSTUS_WEIGHT = 1.8
    SNAP_WEIGHT     = 1.2

    /********************************************************************************
     ********************************************************************************
     ***** Do not edit following settings *******************************************
     ********************************************************************************
     ********************************************************************************/

    OPREFIX   = "ginger"
    PDIR_PREP = "${PDIR}/Prep"
    PDIR_PREP_MAPPING = "${PDIR}/Prep/mapping"
    PDIR_PREP_MAPPING_MAPPING = "${PDIR}/Prep/mapping/mapping"
    PDIR_PREP_MAPPING_MERGE = "${PDIR}/Prep/mapping/merge"
    PDIR_PREP_MAPPING_TOLEARN1ST = "${PDIR}/Prep/mapping/to_learn_1st"
    PDIR_PREP_MAPPING_TOLEARN2ND = "${PDIR}/Prep/mapping/to_learn_2nd"
    PDIR_PREP_DENOVO = "${PDIR}/Prep/denovo"
    PDIR_PREP_DENOVO_TRINITY = "${PDIR}/Prep/denovo/trinity"
    PDIR_PREP_DENOVO_OASES = "${PDIR}/Prep/denovo/oases"
    PDIR_PREP_HOMOLOGY = "${PDIR}/Prep/homology"
    PDIR_PREP_HOMOLOGY_HOMOLOGY = "${PDIR}/Prep/homology/homology"
    PDIR_PREP_HOMOLOGY_HOMOLOGYMERGE = "${PDIR}/Prep/homology/homology_merge"
    PDIR_PREP_HOMOLOGY_HOMOLOGYFILTER = "${PDIR}/Prep/homology/homology_filter"
    PDIR_PREP_ABINITIO = "${PDIR}/Prep/abinitio"
    PDIR_PREP_ABINITIO_AUGUSTUS = "${PDIR}/Prep/abinitio/augustus"
    PDIR_PREP_ABINITIO_SNAP = "${PDIR}/Prep/abinitio/snap"
    AUGUSTUS_WORK_DIR = "${PDIR}/Prep/augustus_config"

}