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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/sarek
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Started March 2016.
Ported to nf-core May 2019.
Ported to DSL 2 July 2020.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/sarek:
An open-source analysis pipeline to detect germline or somatic variants
from whole genome or targeted sequencing
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/sarek
Website: https://nf-co.re/sarek
Docs : https://nf-co.re/sarek/usage
Slack : https://nfcore.slack.com/channels/sarek
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.ascat_alleles = WorkflowMain.getGenomeAttribute(params, 'ascat_alleles')
params.ascat_genome = WorkflowMain.getGenomeAttribute(params, 'ascat_genome')
params.ascat_loci = WorkflowMain.getGenomeAttribute(params, 'ascat_loci')
params.ascat_loci_gc = WorkflowMain.getGenomeAttribute(params, 'ascat_loci_gc')
params.ascat_loci_rt = WorkflowMain.getGenomeAttribute(params, 'ascat_loci_rt')
params.bwa = WorkflowMain.getGenomeAttribute(params, 'bwa')
params.bwamem2 = WorkflowMain.getGenomeAttribute(params, 'bwamem2')
params.cf_chrom_len = WorkflowMain.getGenomeAttribute(params, 'cf_chrom_len')
params.chr_dir = WorkflowMain.getGenomeAttribute(params, 'chr_dir')
params.dbsnp = WorkflowMain.getGenomeAttribute(params, 'dbsnp')
params.dbsnp_tbi = WorkflowMain.getGenomeAttribute(params, 'dbsnp_tbi')
params.dbsnp_vqsr = WorkflowMain.getGenomeAttribute(params, 'dbsnp_vqsr')
params.dict = WorkflowMain.getGenomeAttribute(params, 'dict')
params.dragmap = WorkflowMain.getGenomeAttribute(params, 'dragmap')
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.fasta_fai = WorkflowMain.getGenomeAttribute(params, 'fasta_fai')
params.germline_resource = WorkflowMain.getGenomeAttribute(params, 'germline_resource')
params.germline_resource_tbi = WorkflowMain.getGenomeAttribute(params, 'germline_resource_tbi')
params.intervals = WorkflowMain.getGenomeAttribute(params, 'intervals')
params.known_snps = WorkflowMain.getGenomeAttribute(params, 'known_snps')
params.known_snps_tbi = WorkflowMain.getGenomeAttribute(params, 'known_snps_tbi')
params.known_snps_vqsr = WorkflowMain.getGenomeAttribute(params, 'known_snps_vqsr')
params.known_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels')
params.known_indels_tbi = WorkflowMain.getGenomeAttribute(params, 'known_indels_tbi')
params.known_indels_vqsr = WorkflowMain.getGenomeAttribute(params, 'known_indels_vqsr')
params.mappability = WorkflowMain.getGenomeAttribute(params, 'mappability')
params.pon = WorkflowMain.getGenomeAttribute(params, 'pon')
params.pon_tbi = WorkflowMain.getGenomeAttribute(params, 'pon_tbi')
params.snpeff_db = WorkflowMain.getGenomeAttribute(params, 'snpeff_db')
params.snpeff_genome = WorkflowMain.getGenomeAttribute(params, 'snpeff_genome')
params.vep_cache_version = WorkflowMain.getGenomeAttribute(params, 'vep_cache_version')
params.vep_genome = WorkflowMain.getGenomeAttribute(params, 'vep_genome')
params.vep_species = WorkflowMain.getGenomeAttribute(params, 'vep_species')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ALTERNATIVE INPUT FILE ON RESTART
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.input_restart = WorkflowSarek.retrieveInput(params, log)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { validateParameters; paramsHelp } from 'plugin/nf-validation'
// Print help message if needed
if (params.help) {
def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GATK.GRCh38 -profile docker --outdir results"
log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
System.exit(0)
}
// Validate input parameters
if (params.validate_params) {
validateParameters()
}
WorkflowMain.initialise(workflow, params, log)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { SAREK } from './workflows/sarek'
// WORKFLOW: Run main nf-core/sarek analysis pipeline
workflow NFCORE_SAREK {
SAREK ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
workflow {
NFCORE_SAREK ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/