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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/raredisease
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/raredisease
Website: https://nf-co.re/raredisease
Slack : https://nfcore.slack.com/channels/raredisease
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.fasta_fai = WorkflowMain.getGenomeAttribute(params, 'fai')
params.bwa_index = WorkflowMain.getGenomeAttribute(params, 'bwa_index')
params.bwamem2_index = WorkflowMain.getGenomeAttribute(params, 'bwamem2')
params.call_interval = WorkflowMain.getGenomeAttribute(params, 'call_interval')
params.gnomad_af = WorkflowMain.getGenomeAttribute(params, 'gnomad_af')
params.gnomad_af_idx = WorkflowMain.getGenomeAttribute(params, 'gnomad_af_idx')
params.gnomad_vcf = WorkflowMain.getGenomeAttribute(params, 'gnomad_vcf')
params.known_dbsnp = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp')
params.known_dbsnp_tbi = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp_tbi')
params.known_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels')
params.known_mills = WorkflowMain.getGenomeAttribute(params, 'known_mills')
params.ml_model = WorkflowMain.getGenomeAttribute(params, 'ml_model')
params.mt_backchain_shift = WorkflowMain.getGenomeAttribute(params, 'mt_backchain_shift')
params.mt_bwamem2_index_shift = WorkflowMain.getGenomeAttribute(params, 'mt_bwamem2_index_shift')
params.mt_fasta_shift = WorkflowMain.getGenomeAttribute(params, 'mt_fasta_shift')
params.mt_fai_shift = WorkflowMain.getGenomeAttribute(params, 'mt_fai_shift')
params.mt_intervals = WorkflowMain.getGenomeAttribute(params, 'mt_intervals')
params.mt_intervals_shift = WorkflowMain.getGenomeAttribute(params, 'mt_intervals_shift')
params.mt_sequence_dictionary_shift = WorkflowMain.getGenomeAttribute(params, 'mt_sequence_dictionary_shift')
params.reduced_penetrance = WorkflowMain.getGenomeAttribute(params, 'reduced_penetrance')
params.sequence_dictionary = WorkflowMain.getGenomeAttribute(params, 'sequence_dictionary')
params.score_config_snv = WorkflowMain.getGenomeAttribute(params, 'score_config_snv')
params.score_config_sv = WorkflowMain.getGenomeAttribute(params, 'score_config_sv')
params.target_bed = WorkflowMain.getGenomeAttribute(params, 'target_bed')
params.svdb_query_dbs = WorkflowMain.getGenomeAttribute(params, 'svdb_query_dbs')
params.variant_catalog = WorkflowMain.getGenomeAttribute(params, 'variant_catalog')
params.vep_filters = WorkflowMain.getGenomeAttribute(params, 'vep_filters')
params.vcfanno_resources = WorkflowMain.getGenomeAttribute(params, 'vcfanno_resources')
params.vcfanno_toml = WorkflowMain.getGenomeAttribute(params, 'vcfanno_toml')
params.vep_cache = WorkflowMain.getGenomeAttribute(params, 'vep_cache')
params.vep_cache_version = WorkflowMain.getGenomeAttribute(params, 'vep_cache_version')
params.gens_interval_list = WorkflowMain.getGenomeAttribute(params, 'gens_interval_list')
params.gens_pon = WorkflowMain.getGenomeAttribute(params, 'gens_pon')
params.gens_gnomad_pos = WorkflowMain.getGenomeAttribute(params, 'gens_gnomad_pos')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
WorkflowMain.initialise(workflow, params, log)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { RAREDISEASE } from './workflows/raredisease'
//
// WORKFLOW: Run main nf-core/raredisease analysis pipeline
//
workflow NFCORE_RAREDISEASE {
RAREDISEASE ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
NFCORE_RAREDISEASE ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/