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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mskilab-org/nf-jabba
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://tanubrata/mskilab-org/nf-jabba
Website: https://nf-co.re/nfcasereports
Slack : https://nfcore.slack.com/channels/nfcasereports
----------------------------------------------------------------------------------------
*/
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')
params.indel_mask = WorkflowMain.getGenomeAttribute(params, 'indel_mask')
params.germ_sv_db = WorkflowMain.getGenomeAttribute(params, 'germ_sv_db')
params.simple_seq_db = WorkflowMain.getGenomeAttribute(params, 'simple_seq_db')
params.blacklist_gridss = WorkflowMain.getGenomeAttribute(params, 'blacklist_gridss')
params.pon_gridss = WorkflowMain.getGenomeAttribute(params, 'pon_gridss')
params.gnomAD_sv_db = WorkflowMain.getGenomeAttribute(params, 'gnomAD_sv_db')
params.junction_pon_gridss = WorkflowMain.getGenomeAttribute(params, 'junction_pon_gridss')
params.junction_pon_svaba = WorkflowMain.getGenomeAttribute(params, 'junction_pon_svaba')
params.gcmapdir_frag = WorkflowMain.getGenomeAttribute(params, 'gcmapdir_frag')
params.build_dryclean = WorkflowMain.getGenomeAttribute(params, 'build_dryclean')
params.hapmap_sites = WorkflowMain.getGenomeAttribute(params, 'hapmap_sites')
params.genome_ver_amber = WorkflowMain.getGenomeAttribute(params, 'genome_ver_amber')
params.het_sites_amber = WorkflowMain.getGenomeAttribute(params, 'het_sites_amber')
params.gc_profile = WorkflowMain.getGenomeAttribute(params, 'gc_profile')
params.diploid_bed = WorkflowMain.getGenomeAttribute(params, 'diploid_bed')
params.pon_dryclean = WorkflowMain.getGenomeAttribute(params, 'pon_dryclean')
params.ref_genome_version = WorkflowMain.getGenomeAttribute(params, 'ref_genome_version')
params.ensembl_data_dir = WorkflowMain.getGenomeAttribute(params, 'ensembl_data_dir')
params.somatic_hotspots = WorkflowMain.getGenomeAttribute(params, 'somatic_hotspots')
params.germline_hotspots = WorkflowMain.getGenomeAttribute(params, 'germline_hotspots')
params.panel_bed = WorkflowMain.getGenomeAttribute(params, 'panel_bed')
params.high_confidence_bed = WorkflowMain.getGenomeAttribute(params, 'high_confidence_bed')
params.sage_pon = WorkflowMain.getGenomeAttribute(params, 'sage_pon')
params.sage_blocklist_regions = WorkflowMain.getGenomeAttribute(params, 'sage_blocklist_regions')
params.sage_blocklist_sites = WorkflowMain.getGenomeAttribute(params, 'sage_blocklist_sites')
params.sage_clinvar_annotations = WorkflowMain.getGenomeAttribute(params, 'sage_clinvar_annotations')
params.gnomAD_snv_db = WorkflowMain.getGenomeAttribute(params, 'gnomAD_snv_db')
params.gnomAD_snv_db_tbi = WorkflowMain.getGenomeAttribute(params, 'gnomAD_snv_db_tbi')
params.sage_germline_pon = WorkflowMain.getGenomeAttribute(params, 'sage_germline_pon')
params.sage_germline_pon_tbi = WorkflowMain.getGenomeAttribute(params, 'sage_germline_pon_tbi')
params.sigprofilerassignment_genome = WorkflowMain.getGenomeAttribute(params, 'sigprofilerassignment_genome')
params.sigprofilerassignment_cosmic_version = WorkflowMain.getGenomeAttribute(params, 'sigprofilerassignment_cosmic_version')
params.segment_mappability = WorkflowMain.getGenomeAttribute(params, 'segment_mappability')
params.driver_gene_panel = WorkflowMain.getGenomeAttribute(params, 'driver_gene_panel')
params.ensembl_data_resources = WorkflowMain.getGenomeAttribute(params, 'ensembl_data_resources')
params.gnomad_resource = WorkflowMain.getGenomeAttribute(params, 'gnomad_resource')
params.blacklist_coverage_jabba = WorkflowMain.getGenomeAttribute(params, 'blacklist_coverage_jabba')
params.gencode_fusions = WorkflowMain.getGenomeAttribute(params, 'gencode_fusions')
params.build_non_integer_balance = WorkflowMain.getGenomeAttribute(params, 'build_non_integer_balance')
params.mask_non_integer_balance = WorkflowMain.getGenomeAttribute(params, 'mask_non_integer_balance')
params.mask_lp_phased_balance = WorkflowMain.getGenomeAttribute(params, 'mask_lp_phased_balance')
params.ref_hrdetect = WorkflowMain.getGenomeAttribute(params, 'ref_hrdetect')
//params.blacklist_junctions_jabba = WorkflowMain.getGenomeAttribute(params, 'blacklist_junctions_jabba')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ALTERNATIVE INPUT FILE ON RESTART
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.input_restart = WorkflowNfcasereports.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 GRCh37 -profile docker"
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 { NFCASEREPORTS } from './workflows/nfcasereports'
//
// WORKFLOW: Run main mskilab-org/nf-jabba analysis pipeline
//
workflow MSKILABORG_NFCASEREPORTS {
NFCASEREPORTS ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
MSKILABORG_NFCASEREPORTS ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/