// SPDX-License-Identifier: MPL-2.0
// Configuration of the FAIR-bioHeaders workflow (main.nf). Dockstore reads the
// manifest block; .dockstore.yml at the repository root points here.

manifest {
    name            = 'FAIR-bioHeaders/FAIR-bioHeaders-Tools'
    description     = 'Add FAIR-bioHeaders (FHR, FHGFF3) metadata headers to FASTA, GFA or GFF3 files and verify them'
    homePage        = 'https://github.com/FAIR-bioHeaders/FAIR-bioHeaders-Tools'
    mainScript      = 'main.nf'
    nextflowVersion = '>=25.04.0'
    version         = '0.8.5'
    license         = 'MPL-2.0'
    author          = 'David Molik, Adam Wright'
    contributors    = [
        [name: 'David Molik', affiliation: 'USDA ARS ABADRU', email: 'molik@fhref.org', orcid: 'https://orcid.org/0000-0003-3192-6538', contribution: ['author', 'maintainer']],
        [name: 'Adam Wright', affiliation: 'OICR', email: 'wright@fhref.org', orcid: 'https://orcid.org/0000-0002-5719-4024', contribution: ['author', 'maintainer']],
    ]
}

params {
    // Samplesheet (CSV with the columns id,metadata,sequence), or one file given by
    // metadata and sequence (and optionally id).
    input    = null
    metadata = null
    sequence = null
    id       = null
    outdir   = 'results'
}

// The fair-bioheaders release the workflow runs. Both processes use the modules'
// BioContainers image (docker, singularity, apptainer); since 0.8.2 it includes the
// optional pyld dependency (the jsonld extra) that reading JSON-LD in other than the
// canonical form needs, such as expanded JSON-LD. The conda profile uses
// environment.yml, which pins the same Bioconda package as the modules (it includes
// pyld too). Keep that pin equal to the modules' pins.
process {
    cpus   = 1
    memory = '2.GB'
    time   = '1.h'

    withName: 'FAIRBIOHEADERS_.*' {
        conda = "${projectDir}/environment.yml"
    }
    withName: 'FAIRBIOHEADERS_COMBINE' {
        publishDir = [path: { "${params.outdir}/combine" }, mode: 'copy']
    }
    withName: 'FAIRBIOHEADERS_VERIFY' {
        publishDir = [path: { "${params.outdir}/verify" }, mode: 'copy']
    }
}

profiles {
    docker {
        docker.enabled    = true
        docker.runOptions = '-u $(id -u):$(id -g)'
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
    }
    apptainer {
        apptainer.enabled    = true
        apptainer.autoMounts = true
    }
    conda {
        conda.enabled  = true
        conda.channels = ['conda-forge', 'bioconda']
    }
    test {
        params.input = "${projectDir}/assets/test/samplesheet.csv"
    }
}