nextflow.config

manifest {
    mainScript = "main.nf"
}

plugins {
    id 'nf-amazon'
}

params {
    outdir = "motus_pipeline_results"

    // --- dbs
    databases = 'nextflow-autodownload-databases'
    download_ftp_path = 'ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs'

    // --- INPUTS
    sample_name = ''
    reads_accession = ''
    single_end = ''
    paired_end_forward = ''
    paired_end_reverse = ''
    mode = '' // single or paired

    // --- fastp filtering ---
    length_filter = 10
    polya_trim = 10
    qualified_quality_phred = 15
    unqualified_percent_limit = 10

    // --- REFERENCE GENOME --- //
    // TODO: we need to list all the genomes we can make
    //       available on the FTP, each one with the corresponding
    //       version and instructions to reconstruct.
    decontamination_indexes_folder = 'hg38'
    decontamination_reference_index = 'hg38.fa'

    // --- custom reference //
    reference_genome = false
    reference_genome_name = false

    // --- CMSEARCH ---
    cmsearch_db_name = 'rfam_models'
    ribosomal_model_path = 'ribosomal_models/ribo.cm'
    ribosomal_claninfo_path = 'ribosomal_models/ribo.claninfo'
    other_model_path = 'other_models'
    other_claninfo_path = 'other_models/other.claninfo'

    // --- mOTUs
    motus_db_name = 'db_mOTU'

    // --- MAPSEQ ---
    // --- download values
    silva_ssu_db_name = 'silva_ssu-20200130'
    ssu_db_fasta = "SSU.fasta"
    ssu_db_tax = "slv_ssu_filtered2.txt"
    ssu_db_otu = "ssu2.otu"
    ssu_label = "SSU"

    silva_lsu_db_name = 'silva_lsu-20200130'
    lsu_db_fasta = "LSU.fasta"
    lsu_db_tax = "slv_lsu_filtered2.txt"
    lsu_db_otu = "lsu2.otu"
    lsu_label = "LSU"

    // --- custom ssh/lsu database --- //
    ssu_db = false
    lsu_db = false
}

profiles {

    aws {
        process {
            executor = 'awsbatch'
            queue = 'nextflow_queue'
        }

        aws {
            batch {
                // NOTE: this setting is only required if the AWS CLI tool is installed in a custom AMI
                cliPath = '/home/ec2-user/miniconda/bin/aws'
                maxParallelTransfers = 2
                maxTransferAttempts = 2
            }
            region = 'eu-west-1'
        }

        workDir = 's3://mgnify-nf/nextflow_env'

        includeConfig 'config/aws.config'
    }

    lsf {
        workDir = params.workdir
        executor {
            name = "lsf"
            queueSize = 200
        }
        process.cache = "lenient"
    }
    singularity {
        singularity {
            enabled = true
            autoMounts = true
            cacheDir = params.singularity_cachedir
        }
    }

    ebi_no_db {
        params {
            outdir = "motus_pipeline_results"
            databases = "nextflow-autodownload-databases"

            sample_name = ""
            single_end = ""
            paired_end_forward = ""
            paired_end_reverse = ""
            mode = ""

            workdir = "/hps/nobackup/rdf/metagenomics/service-team/nextflow-workdir/motus-pipeline"
            singularity_cachedir = "/hps/nobackup/rdf/metagenomics/service-team/singularity-cache/"
        }
        workDir = params.workdir

        executor {
            name = "lsf"
            queueSize = 200
        }
        process.cache = "lenient"
        includeConfig 'config/codon.config'
    }

    ebi {
        params {
            outdir = "motus_pipeline_results"
            databases = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/"

            sample_name = ""
            single_end = ""
            paired_end_forward = ""
            paired_end_reverse = ""
            mode = ""

            workdir = "/hps/nobackup/rdf/metagenomics/nextflow-jobstore/motus_pipeline"
            singularity_cachedir = "/hps/nobackup/rdf/metagenomics/singularity_cache_nextflow/"

            reference_genome = '/hps/nobackup/rdf/metagenomics/service-team/ref-dbs/bwa-mem2/'
            reference_genome_name = 'hg38.fa'

            motus_db = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/mgnify-v5/mOTUs/db_mOTU_v3.0.1/db_mOTU"

            ssu_db = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/mgnify-v5/silva_ssu/"
            lsu_db = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/mgnify-v5/silva_lsu/"

            rfam_ribo_models = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/mgnify-v5/Rfam/ribosomal/ribo.cm"
            rfam_other_models = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/mgnify-v5/Rfam/other/*.cm"
            rfam_ribo_clan = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/mgnify-v5/Rfam/ribosomal/ribo.claninfo"
            rfam_other_clan = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/mgnify-v5/Rfam/other/other.claninfo"
        }
        workDir = params.workdir

        executor {
            name = "lsf"
            queueSize = 200
        }
        process.cache = "lenient"

        includeConfig 'config/codon.config'
    }

    local {
         docker {
            enabled = true
            autoMounts = true
            fixOwnership = true
        }
        executor {
            name = "local"
            cpus = 2
        }

        includeConfig 'config/local.config'
    }
}