tools/nf_core/pipeline-template/main.nf at 75e8484a3d23234081f22fac1498a067586d9b0e · nf-core/tools · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    {{ name }}
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/{{ name }}
{%- if is_nfcore %}
    Website: https://nf-co.re/{{ short_name }}
    Slack  : https://nfcore.slack.com/channels/{{ short_name }}
{%- endif %}
----------------------------------------------------------------------------------------
*/

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
{%- if modules %}
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
{%- if igenomes %}
include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// TODO nf-core: Remove this line if you don't need a FASTA file
//   This is an example of how to use getGenomeAttribute() to fetch parameters
//   from igenomes.config using `--genome`
params.fasta = getGenomeAttribute('fasta')
{% endif %}{% endif %}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {

    take:
    samplesheet // channel: samplesheet read in from --input

    main:

    //
    // WORKFLOW: Run pipeline
    //
    {{ short_name|upper }} (
        samplesheet,
        {%- if multiqc %}
        params.multiqc_config,
        params.multiqc_logo,
        params.multiqc_methods_description,
        {%- endif %}
        params.outdir,
    )
{%- if multiqc %}{%- if modules %}
    emit:
    multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
    multiqc_data   = {{ short_name|upper }}.out.multiqc_data // channel: [meta, /path/to/multiqc_data/]
    multiqc_plots  = {{ short_name|upper }}.out.multiqc_plots // channel: [meta, /path/to/multiqc_plots/]
{%- endif %}{%- endif %}
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

    main:

    {%- if modules %}
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input{% if nf_schema %},
        params.help,
        params.help_full,
        params.show_hidden{% endif %}
    )
    {%- endif %}

    //
    // WORKFLOW: Run main workflow
    //
    {{ prefix_nodash|upper }}_{{ short_name|upper }} (
        {%- if modules %}
        PIPELINE_INITIALISATION.out.samplesheet
        {%- else %}
        params.input
        {%- endif %}
    )

    {%- if modules %}
    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        {%- if email %}
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        {%- endif %}
        params.outdir,
        params.monochrome_logs,
        {%- if multiqc %}
        {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
    )
    {%- endif %}
{%- if multiqc %}{%- if modules %}

    def multiqc_publish = {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report
        .mix({{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_data)
        .mix({{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_plots)

    publish:
    multiqc = multiqc_publish
}

output {
    multiqc {
        path "multiqc"
    }
{%- endif %}{%- endif %}

}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/