From 0b3d82dd3b09b8c9bb0bd94734b903fa65299177 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 9 Apr 2024 18:09:50 +0200 Subject: [PATCH] collect --- main.nf | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/main.nf b/main.nf index f797290bbc..8b7940a558 100755 --- a/main.nf +++ b/main.nf @@ -82,28 +82,28 @@ include { PREPARE_REFERENCE_CNVKIT } from './subworkflows/local/prepare_ fasta = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() // Initialize file channels based on params, defined in the params.genomes[params.genome] scope -bcftools_annotations = params.bcftools_annotations ? Channel.fromPath(params.bcftools_annotations).collect() : Channel.empty() -bcftools_header_lines = params.bcftools_header_lines ? Channel.fromPath(params.bcftools_header_lines).collect() : Channel.empty() -cf_chrom_len = params.cf_chrom_len ? Channel.fromPath(params.cf_chrom_len) : [] -dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.value([]) -fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : Channel.empty() -germline_resource = params.germline_resource ? Channel.fromPath(params.germline_resource) : Channel.value([]) // Mutect2 does not require a germline resource, so set to optional input -known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.value([]) -known_snps = params.known_snps ? Channel.fromPath(params.known_snps).collect() : Channel.value([]) -mappability = params.mappability ? Channel.fromPath(params.mappability) : Channel.value([]) -pon = params.pon ? Channel.fromPath(params.pon) : Channel.value([]) // PON is optional for Mutect2 (but highly recommended) -sentieon_dnascope_model = params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model) : Channel.value([]) +bcftools_annotations = params.bcftools_annotations ? Channel.fromPath(params.bcftools_annotations).collect() : Channel.empty() +bcftools_header_lines = params.bcftools_header_lines ? Channel.fromPath(params.bcftools_header_lines).collect() : Channel.empty() +cf_chrom_len = params.cf_chrom_len ? Channel.fromPath(params.cf_chrom_len).collect() : [] +dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.value([]) +fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : Channel.empty() +germline_resource = params.germline_resource ? Channel.fromPath(params.germline_resource).collect() : Channel.value([]) // Mutect2 does not require a germline resource, so set to optional input +known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.value([]) +known_snps = params.known_snps ? Channel.fromPath(params.known_snps).collect() : Channel.value([]) +mappability = params.mappability ? Channel.fromPath(params.mappability).collect() : Channel.value([]) +pon = params.pon ? Channel.fromPath(params.pon).collect() : Channel.value([]) // PON is optional for Mutect2 (but highly recommended) +sentieon_dnascope_model = params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect() : Channel.value([]) // Initialize value channels based on params, defined in the params.genomes[params.genome] scope -ascat_genome = params.ascat_genome ?: Channel.empty() -dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.dbsnp_vqsr) : Channel.empty() -known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_indels_vqsr) : Channel.empty() -known_snps_vqsr = params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() -ngscheckmate_bed = params.ngscheckmate_bed ? Channel.value(params.ngscheckmate_bed) : Channel.empty() -snpeff_db = params.snpeff_db ?: Channel.empty() -vep_cache_version = params.vep_cache_version ?: Channel.empty() -vep_genome = params.vep_genome ?: Channel.empty() -vep_species = params.vep_species ?: Channel.empty() +ascat_genome = params.ascat_genome ?: Channel.empty() +dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.dbsnp_vqsr) : Channel.empty() +known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_indels_vqsr) : Channel.empty() +known_snps_vqsr = params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() +ngscheckmate_bed = params.ngscheckmate_bed ? Channel.value(params.ngscheckmate_bed) : Channel.empty() +snpeff_db = params.snpeff_db ?: Channel.empty() +vep_cache_version = params.vep_cache_version ?: Channel.empty() +vep_genome = params.vep_genome ?: Channel.empty() +vep_species = params.vep_species ?: Channel.empty() vep_extra_files = []