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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ajandria/futuriandge - Bulk RNA-seq pipeline for differential gene expression analysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/ajandria/futuriandge
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// Initial params
params.contrasts = null // if null dont run DESeq2 downstream subworkflow
params.input = null
params.outDir = "${baseDir}/results"
params.organism = null
// Constant for rRNA screening using SILVA dbs
params.rRNA_db_path = '/archive/users/ajan/references/rRNA_databases'
if (params.organism == null) {
error "params.organism was not provided. Please specify an organism."
} else if (params.organism == 'human') {
println("Organism is human")
params.reference_genome = '/archive/users/ajan/references/Homo_sapiens_GRCh38_109/Homo_sapiens.GRCh38.109_genomeDir_STAR_2.7.10b'
params.gtf = '/archive/users/ajan/references/Homo_sapiens_GRCh38_109/Homo_sapiens.GRCh38.109.chr.gtf'
params.refFlat = '/archive/users/ajan/references/Homo_sapiens_GRCh38_109/Homo_sapiens.GRCh38.109.chr.gtf.gz.refflat.gz'
params.gene_map = '/archive/users/ajan/references/Homo_sapiens_GRCh38_109/homo_sapiens_salmon_1.10.1/txp2gene.tsv'
params.salmon_index = '/archive/users/ajan/references/Homo_sapiens_GRCh38_109/homo_sapiens_salmon_1.10.1/salmon_index-with_decoys'
} else if (params.organism == 'mouse') {
println("Organism is mouse")
params.reference_genome = '/archive/users/ajan/references/Mus_musculus.GRCm39.108/Mus_musculus.GRCm39.108_genomeDir_STAR_2.7.10b'
params.gtf = '/archive/users/ajan/references/Mus_musculus.GRCm39.108/Mus_musculus.GRCm39.108.chr.gtf'
params.refFlat = '/archive/users/ajan/references/Mus_musculus.GRCm39.108/Mus_musculus.GRCm39.108.chr.gtf.refFlat.gz'
params.gene_map = '/archive/users/ajan/references/Mus_musculus.GRCm39.108/salmon_1.10_1/txp2gene.tsv'
params.salmon_index = '/archive/users/ajan/references/Mus_musculus.GRCm39.108/salmon_1.10_1/salmon_index'
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
WorkflowMain.initialise(workflow, params, log)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EXECUTE WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// log.info """\
// ====================================================================================================================
// U N I F O R M A L B U L K R N A - S E Q D I F F E R E N T I A L G E N E
// E X P R E S S I O N A N A L Y S I S P I P E L I N E
// V e r s i o n: 0 . 0 . 1 . d
// =====================================================================================================================
// |
// | Sample sheet : $params.input
// |
// =====================================================================================================================
// """.stripIndent()
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { UNIFORMAL } from "${baseDir}/workflows/run_processing.nf"
//
// WORKFLOW: Run main ajandria/futuriandge analysis pipeline
//
workflow FUTURIANDGE {
UNIFORMAL()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
FUTURIANDGE()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/