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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
plant-food-research-open/genepal
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/plant-food-research-open/genepal
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { GENEPAL } from './workflows/genepal'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_genepal_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_genepal_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow PLANTFOODRESEARCHOPEN_GENEPAL {
take:
ch_target_assembly
ch_tar_assm_str
ch_is_masked
ch_te_library
ch_braker_annotation
ch_braker_ex_asm_str
ch_benchmark_gff
ch_rna_sra
ch_rna_fq
ch_rna_bam_by_assembly
ch_sortmerna_fastas
ch_ext_prot_fastas
ch_liftoff_fasta
ch_liftoff_gff
ch_tsebra_config
ch_orthofinder_pep
main:
//
// WORKFLOW: Run pipeline
//
GENEPAL(
ch_target_assembly,
ch_tar_assm_str,
ch_is_masked,
ch_te_library,
ch_braker_annotation,
ch_braker_ex_asm_str,
ch_benchmark_gff,
ch_rna_sra,
ch_rna_fq,
ch_rna_bam_by_assembly,
ch_sortmerna_fastas,
ch_ext_prot_fastas,
ch_liftoff_fasta,
ch_liftoff_gff,
ch_tsebra_config,
ch_orthofinder_pep
)
emit:
multiqc_report = GENEPAL.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.monochrome_logs,
args,
params.outdir,
params.input,
params.rna_evidence,
params.liftoff_annotations,
params.orthofinder_annotations
)
//
// WORKFLOW: Run main workflow
//
PLANTFOODRESEARCHOPEN_GENEPAL(
PIPELINE_INITIALISATION.out.target_assembly,
PIPELINE_INITIALISATION.out.tar_assm_str,
PIPELINE_INITIALISATION.out.is_masked,
PIPELINE_INITIALISATION.out.te_library,
PIPELINE_INITIALISATION.out.braker_annotation,
PIPELINE_INITIALISATION.out.braker_ex_asm_str,
PIPELINE_INITIALISATION.out.benchmark_gff,
PIPELINE_INITIALISATION.out.rna_sra,
PIPELINE_INITIALISATION.out.rna_fq,
PIPELINE_INITIALISATION.out.rna_bam_by_assembly,
PIPELINE_INITIALISATION.out.sortmerna_fastas,
PIPELINE_INITIALISATION.out.ext_prot_fastas,
PIPELINE_INITIALISATION.out.liftoff_fasta,
PIPELINE_INITIALISATION.out.liftoff_gff,
PIPELINE_INITIALISATION.out.tsebra_config,
PIPELINE_INITIALISATION.out.orthofinder_pep
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
PLANTFOODRESEARCHOPEN_GENEPAL.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/