nanotranseq/main.nf at dev · nfdata-omics/nanotranseq · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nfdata-omics/nanotranseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/nfdata-omics/nanotranseq
----------------------------------------------------------------------------------------
*/

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

include { NANOTRANSEQ  } from './workflows/nanotranseq'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_nanotranseq_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_nanotranseq_pipeline'
include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_nanotranseq_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')
params.gtf = getGenomeAttribute('gtf')
params.minimap2_index = getGenomeAttribute('minimap2')

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFDATAOMICS_NANOTRANSEQ {

    take:
    samplesheet // channel: samplesheet read in from --input
    fasta       // channel: fasta read in from --fasta
    gtf         // channel: GTF file read in from --gtf
    gene_id     // channel: attributed gene ID
    gene_attributes     // channel: extra gene attributes
    transcript_fasta    // channel: transcript fasta file read in from --transcript_fasta
    direct_rna  // channel: direct_rna read in from --direct_rna
    minimap2_index  // channel: minimap2_index read in from --minimap2_index
    formula       // channel: formula read in from --deseq2_formula
    comparison    // channel: comparison read in from --deseq2_comparison
    fdr_threshold // channel: fdr_threshold read in from --deseq2_fdr_threshold

    main:

    //
    // WORKFLOW: Run pipeline
    //
    NANOTRANSEQ (
        samplesheet,
        fasta,
        gtf,
        gene_id,
        gene_attributes,
        transcript_fasta,
        direct_rna,
        minimap2_index,
        formula,
        comparison,
        fdr_threshold
    )
    emit:
    multiqc_report = NANOTRANSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input,
        params.fasta,
        params.gtf,
        params.gene_id,
        params.gene_attributes,
        params.transcript_fasta,
        params.direct_rna,
        params.minimap2_index,
        params.deseq2_formula,
        params.deseq2_comparisons,
        params.deseq2_fdr,
        params.help,
        params.help_full,
        params.show_hidden
    )

    //
    // WORKFLOW: Run main workflow
    //
    NFDATAOMICS_NANOTRANSEQ (
        PIPELINE_INITIALISATION.out.samplesheet,
        PIPELINE_INITIALISATION.out.fasta,
        PIPELINE_INITIALISATION.out.gtf,
        PIPELINE_INITIALISATION.out.gene_id,
        PIPELINE_INITIALISATION.out.gene_attributes,
        PIPELINE_INITIALISATION.out.transcript_fasta,
        PIPELINE_INITIALISATION.out.direct_rna,
        PIPELINE_INITIALISATION.out.minimap2_index,
        PIPELINE_INITIALISATION.out.formula,
        PIPELINE_INITIALISATION.out.comparison,
        PIPELINE_INITIALISATION.out.fdr_threshold
    )
    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        NFDATAOMICS_NANOTRANSEQ.out.multiqc_report
    )
}

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