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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sanger-tol/longreadmag
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/sanger-tol/longreadmag
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { LONGREADMAG } from './workflows/longreadmag'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_longreadmag_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_longreadmag_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow SANGERTOL_LONGREADMAG {
take:
pacbio_fasta // channel: pacbio fasta read in from --input
assembly // channel: pre-existing assembly read in from --input
hic_cram // channel: hic cram read in from --input
hic_enzymes // channel: hic enzymes read in from --input
rfam_rrna_cm // channel: rrna cm file from params.rfam_rrna_cm
magscot_gtdb_hmm_db // channel: hmms for magscot
checkm2_db // channel: checkm2 db from --params.checkm2_db
gtdbtk_db // channel: gtdbtk db from --params.gtdbtk_db
gtdbtk_mash_db // channel: gtdbtk mash db from --params.gtdbtk_mash_db
main:
//
// WORKFLOW: Run pipeline
//
LONGREADMAG (
pacbio_fasta,
assembly,
hic_cram,
hic_enzymes,
rfam_rrna_cm,
magscot_gtdb_hmm_db,
checkm2_db,
gtdbtk_db,
gtdbtk_mash_db
)
// emit:
// multiqc_report = LONGREADMAG.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
)
//
// WORKFLOW: Run main workflow
//
SANGERTOL_LONGREADMAG (
PIPELINE_INITIALISATION.out.pacbio_fasta,
PIPELINE_INITIALISATION.out.assembly,
PIPELINE_INITIALISATION.out.hic_cram,
PIPELINE_INITIALISATION.out.hic_enzymes,
PIPELINE_INITIALISATION.out.rfam_rrna_cm,
PIPELINE_INITIALISATION.out.magscot_gtdb_hmm_db,
PIPELINE_INITIALISATION.out.checkm2_db,
PIPELINE_INITIALISATION.out.gtdbtk_db,
PIPELINE_INITIALISATION.out.gtdbtk_mash_db
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
params.outdir,
params.monochrome_logs,
[]
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/