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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
qbic-pipelines/rnadeseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/qbic-pipelines/rnadeseq
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_rnadeseq_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//Either genome needs to be set or the parameters gtf (for rsem/salmon) and organism, species_library and keytype
//(for pathway analysis) have to be provided separately
//-->gtf is necessary for rsem and salmon
if (params.input_type in ["rsem", "salmon"]) {
if (!params.genome && !params.gtf) { exit 1, 'Please provide either genome or gtf file!' }
else if (!params.gtf) {
params.gtf = getGenomeAttribute('gtf')
if (!params.gtf) {
exit 1, 'It seems that for your genome, no gtf file is defined. Please provide a gtf with the --gtf parameter or open a github issue: https://github.com/qbic-pipelines/rnadeseq/issues'
}
}
}
//-->organism, species_library and keytype are necessary for pathway analysis
if (params.run_pathway_analysis) {
if (!params.genome && !params.organism) { exit 1, 'Please provide either genome or organism!' }
else if (!params.organism) {
params.organism = getGenomeAttribute('organism')
if (!params.organism) {
exit 1, 'It seems that for your genome, no organism is defined. Please provide the organism with the --organism parameter or open a github issue: https://github.com/qbic-pipelines/rnadeseq/issues'
}
}
if (!params.genome && !params.species_library) { exit 1, 'Please provide either genome or species_library!' }
else if (!params.species_library) {
params.species_library = getGenomeAttribute('species_library')
if (!params.species_library) {
exit 1, 'It seems that for your genome, no species_library is defined. Please provide the library with the --species_library parameter or open a github issue: https://github.com/qbic-pipelines/rnadeseq/issues'
}
}
if (!params.genome && !params.keytype) { exit 1, 'Please provide either genome or keytype!' }
else if (!params.keytype) {
params.keytype = getGenomeAttribute('keytype')
if (!params.keytype) {
exit 1, 'It seems that for your genome, no keytype is defined. Please provide the keytype with the --keytype parameter or open a github issue: https://github.com/qbic-pipelines/rnadeseq/issues'
}
}
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { RNADESEQ } from './workflows/rnadeseq'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow QBIC_RNADESEQ {
main:
//
// WORKFLOW: Run pipeline
//
RNADESEQ ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// WORKFLOW: Run main workflow
//
QBIC_RNADESEQ ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/