collect

nf-core · Apr 9, 2024 · 0b3d82d · 0b3d82d
1 parent c2d1fd4
commit 0b3d82d
Showing 1 changed file with 20 additions and 20 deletions.
diff --git 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 = []