params {
    help = false
    version = false

    fastq = null
    bam = null
    sample = null
    sample_sheet = null
    out_dir = "output"
    igv = false

    ref_genome = null
    ref_annotation = null
    transcriptome_mode = "discover"
    direct_rna = false

    de_analysis = false
    condition_column = "condition"
    covariates = null
    reference_level = null

    analyse_unclassified = false
    analyse_fail = false
    fastq_chunk = null

    threads = 4
    minimap2_index_opts = ""
    minimap2_opts = ""
    ndr = null
    skip_sqanti = false
    sqanti_skip_orf = true
    sqanti_extra_args = ""

    aws_image_prefix = null
    aws_queue = null
    disable_ping = false

    monochrome_logs = false
    validate_params = true
    show_hidden_params = false

    schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,store_dir'

    wf {
        keep_unaligned = true
        return_fastq = true
        per_read_stats = false
        allow_multiple_basecall_models = false
        example_cmd = [
            "--de_analysis",
            "--direct_rna",
            "--fastq 'wf-transcriptomes-demo/differential_expression_fastq'",
            "--minimap2_index_opts '-k 15'",
            "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
            "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
            "--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'",
        ]
        common_sha = "sha21d552f9910c575766e5d465fcb7b52fefda4b79"
        container_sha = "sha02e44f706d88fa29d8344b78479f187db7eec4ec"
        sqanti_sha = "sha5bd775836492699e2537ebf846098eb117191d87"
        agent = null
        epi2me_instance = null
        epi2me_user = null
    }
}

manifest {
    name            = 'epi2me-labs/wf-transcriptomes'
    author          = 'Oxford Nanopore Technologies'
    homePage        = 'https://github.com/epi2me-labs/wf-transcriptomes'
    description     = 'Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq.'
    mainScript      = 'main.nf'
    nextflowVersion = '>=23.04.2'
    version         = 'v0.1.0'
}

process {
    withLabel:wf_common {
        container = "ontresearch/wf-common:${params.wf.common_sha}"
    }
    withLabel:wf_transcriptomes {
        container = "ontresearch/wf-transcriptomes-core:${params.wf.container_sha}"
    }
    withLabel:wf_transcriptomes_sqanti {
        container = "ontresearch/wf-transcriptomes-sqanti:${params.wf.sqanti_sha}"
    }
    shell = ['/bin/bash', '-euo', 'pipefail']
}

profiles {
    standard {
        docker {
            enabled = true
            runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
        }
    }

    singularity {
        singularity {
            enabled = true
            autoMounts = true
        }
    }

    conda {
        conda.enabled = true
    }

    awsbatch {
        process {
            executor = 'awsbatch'
            queue = "${params.aws_queue}"
            withLabel:wf_common {
                container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"
                memory = '8G'
            }
            withLabel:wf_transcriptomes {
                container = "${params.aws_image_prefix}-wf-transcriptomes-core:${params.wf.container_sha}"
            }
            withLabel:wf_transcriptomes_sqanti {
                container = "${params.aws_image_prefix}-wf-transcriptomes-sqanti:${params.wf.sqanti_sha}"
            }
            shell = ['/bin/bash', '-euo', 'pipefail']
        }
    }

    local {
        process.executor = 'local'
    }
}

epi2melabs {
    tags = "wf-transcriptomes,transcriptomics,rna"
    icon = "faDna"
}

timeline {
    enabled = true
    overwrite = true
    file = "${params.out_dir}/execution/timeline.html"
}

report {
    enabled = true
    overwrite = true
    file = "${params.out_dir}/execution/report.html"
}

trace {
    enabled = true
    overwrite = true
    file = "${params.out_dir}/execution/trace.txt"
}

env {
    PYTHONNOUSERSITE = 1
    JAVA_TOOL_OPTIONS = "-Xlog:disable -Xlog:all=warning:stderr"
    R_BIOC_VERSION = "3.21"
    BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = "FALSE"
}