diff --git a/conf/genomes.config b/conf/genomes.config index 1ba761b8e9..834c8536b8 100644 --- a/conf/genomes.config +++ b/conf/genomes.config @@ -10,89 +10,89 @@ params { genomes { 'GRCh37' { - ac_loci = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci" - ac_loci_gc = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci.gc" - bwa = "${params.genomes_base}/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}" - chr_dir = "${params.genomes_base}/Chromosomes" - chr_length = "${params.genomes_base}/human_g1k_v37_decoy.len" - dbsnp = "${params.genomes_base}/dbsnp_138.b37.vcf" - dbsnp_index = "${params.genomes_base}/dbsnp_138.b37.vcf.idx" - dict = "${params.genomes_base}/human_g1k_v37_decoy.dict" - fasta = "${params.genomes_base}/human_g1k_v37_decoy.fasta" - fasta_fai = "${params.genomes_base}/human_g1k_v37_decoy.fasta.fai" - germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz" - germline_resource_index = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi" - intervals = "${params.genomes_base}/wgs_calling_regions_Sarek.list" - known_indels = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf" - known_indels_index = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx" - mappability = "${params.genomes_base}/out100m2_hg19.gem" - snpeff_db = 'GRCh37.75' - vep_genome = 'GRCh37' - vep_species = 'homo_sapiens' - vep_cache_version = '104' + ac_loci = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci" + ac_loci_gc = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci.gc" + bwa = "${params.genomes_base}/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}" + chr_dir = "${params.genomes_base}/Chromosomes" + chr_length = "${params.genomes_base}/human_g1k_v37_decoy.len" + dbsnp = "${params.genomes_base}/dbsnp_138.b37.vcf" + dbsnp_tbi = "${params.genomes_base}/dbsnp_138.b37.vcf.idx" + dict = "${params.genomes_base}/human_g1k_v37_decoy.dict" + fasta = "${params.genomes_base}/human_g1k_v37_decoy.fasta" + fasta_fai = "${params.genomes_base}/human_g1k_v37_decoy.fasta.fai" + germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz" + germline_resource_tbi = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi" + intervals = "${params.genomes_base}/wgs_calling_regions_Sarek.list" + known_indels = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf" + known_indels_tbi = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx" + mappability = "${params.genomes_base}/out100m2_hg19.gem" + snpeff_db = 'GRCh37.75' + vep_genome = 'GRCh37' + vep_species = 'homo_sapiens' + vep_cache_version = '104' } 'GRCh38' { - ac_loci = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci" - ac_loci_gc = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci.gc" - bwa = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}" - chr_dir = "${params.genomes_base}/Chromosomes" - chr_length = "${params.genomes_base}/Homo_sapiens_assembly38.len" - dbsnp = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz" - dbsnp_index = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz.tbi" - dict = "${params.genomes_base}/Homo_sapiens_assembly38.dict" - fasta = "${params.genomes_base}/Homo_sapiens_assembly38.fasta" - fasta_fai = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.fai" - germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz" - germline_resource_index = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi" - intervals = "${params.genomes_base}/wgs_calling_regions.hg38.bed" - known_indels = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz" - known_indels_index = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi" - mappability = "${params.genomes_base}/out100m2_hg38.gem" - snpeff_db = 'GRCh38.99' - vep_genome = 'GRCh38' - vep_species = 'homo_sapiens' - vep_cache_version = '104' + ac_loci = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci" + ac_loci_gc = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci.gc" + bwa = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}" + chr_dir = "${params.genomes_base}/Chromosomes" + chr_length = "${params.genomes_base}/Homo_sapiens_assembly38.len" + dbsnp = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz" + dbsnp_tbi = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz.tbi" + dict = "${params.genomes_base}/Homo_sapiens_assembly38.dict" + fasta = "${params.genomes_base}/Homo_sapiens_assembly38.fasta" + fasta_fai = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.fai" + germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz" + germline_resource_tbi = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi" + intervals = "${params.genomes_base}/wgs_calling_regions.hg38.bed" + known_indels = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz" + known_indels_tbi = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi" + mappability = "${params.genomes_base}/out100m2_hg38.gem" + snpeff_db = 'GRCh38.99' + vep_genome = 'GRCh38' + vep_species = 'homo_sapiens' + vep_cache_version = '104' } 'minimalGRCh37' { - fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta" + fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta" } 'smallGRCh37' { - dbsnp = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz" - fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta" - germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.small.PASS.AC.AF.only.vcf.gz" - intervals = "${params.genomes_base}/small.intervals" - known_indels = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz" - snpeff_db = 'GRCh37.75' - vep_genome = 'GRCh37' - vep_species = 'homo_sapiens' - vep_cache_version = '104' + dbsnp = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz" + fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta" + germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.small.PASS.AC.AF.only.vcf.gz" + intervals = "${params.genomes_base}/small.intervals" + known_indels = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz" + snpeff_db = 'GRCh37.75' + vep_genome = 'GRCh37' + vep_species = 'homo_sapiens' + vep_cache_version = '104' } 'smallerGRCh37' { - fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta" - known_indels = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz" + fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta" + known_indels = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz" } 'smallGRCh38' { - dbsnp = "${params.genomes_base}/dbsnp_146_hg38_chr20_tso-only.vcf.gz" - fasta = "${params.genomes_base}/Homo_sapiens_assembly38_chr20.fasta" - known_indels = "${params.genomes_base}/Mills_and_1000G_gold_standard_indels_hg38_chr20.vcf.gz" - snpeff_db = 'GRCh38.99' - vep_genome = 'GRCh38' - vep_species = 'homo_sapiens' - vep_cache_version = '99' + dbsnp = "${params.genomes_base}/dbsnp_146_hg38_chr20_tso-only.vcf.gz" + fasta = "${params.genomes_base}/Homo_sapiens_assembly38_chr20.fasta" + known_indels = "${params.genomes_base}/Mills_and_1000G_gold_standard_indels_hg38_chr20.vcf.gz" + snpeff_db = 'GRCh38.99' + vep_genome = 'GRCh38' + vep_species = 'homo_sapiens' + vep_cache_version = '99' } 'custom' { - fasta = null + fasta = null } 'small_hg38' { - dbsnp = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" - fasta = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta" - fasta_fai = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai" - germline_resource = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" - known_indels = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" - snpeff_db = 'GRCh38.99' - vep_genome = 'GRCh38' - vep_species = 'homo_sapiens' - vep_cache_version = '104' + dbsnp = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + fasta = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta" + fasta_fai = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai" + germline_resource = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" + known_indels = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + snpeff_db = 'GRCh38.99' + vep_genome = 'GRCh38' + vep_species = 'homo_sapiens' + vep_cache_version = '104' } } } diff --git a/conf/igenomes.config b/conf/igenomes.config index b4a54c5918..eda7409f20 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -12,241 +12,241 @@ params { // illumina iGenomes reference file paths genomes { 'GATK.GRCh37' { - ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci" - ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc" - bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}" - chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes" - chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Length/human_g1k_v37_decoy.len" - dbsnp = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf" - dbsnp_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx" - dict = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict" - fasta = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta" - fasta_fai = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai" - germline_resource = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz" - germline_resource_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi" - intervals = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list" - known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf" - known_indels_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx" - mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem" - snpeff_db = 'GRCh37.75' - vep_cache_version = '104' - vep_genome = 'GRCh37' - vep_species = 'homo_sapiens' + ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci" + ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc" + bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}" + chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes" + chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Length/human_g1k_v37_decoy.len" + dbsnp = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf" + dbsnp_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx" + dict = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict" + fasta = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta" + fasta_fai = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai" + germline_resource = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz" + germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi" + intervals = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list" + known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf" + known_indels_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx" + mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem" + snpeff_db = 'GRCh37.75' + vep_cache_version = '104' + vep_genome = 'GRCh37' + vep_species = 'homo_sapiens' } 'GATK.GRCh38' { - ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci" - ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc" - bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}" - chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes" - chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len" - dbsnp = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz" - dbsnp_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi" - dict = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict" - fasta = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta" - fasta_fai = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai" - germline_resource = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz" - germline_resource_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi" - intervals = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed" - known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz" - known_indels_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi" - mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem" - snpeff_db = 'GRCh38.99' - vep_cache_version = '104' - vep_genome = 'GRCh38' - vep_species = 'homo_sapiens' + ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci" + ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc" + bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}" + chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes" + chr_length = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len" + dbsnp = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz" + dbsnp_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi" + dict = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict" + fasta = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta" + fasta_fai = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai" + germline_resource = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz" + germline_resource_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi" + intervals = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed" + known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz" + known_indels_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi" + mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem" + snpeff_db = 'GRCh38.99' + vep_cache_version = '104' + vep_genome = 'GRCh38' + vep_species = 'homo_sapiens' } 'Ensembl.GRCh37' { - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" + bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" + readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" } 'NCBI.GRCh38' { - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" } 'GRCm38' { - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - chr_dir = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes" - chr_length = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Length/GRCm38.len" - dbsnp = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz" - dbsnp_index = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi" - dict = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict" - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - fasta_fai = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai" - intervals = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed" - known_indels = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz" - known_indels_index = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi" - mappability = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - snpeff_db = 'GRCm38.99' - vep_cache_version = '102' - vep_genome = 'GRCm38' - vep_species = 'mus_musculus' + bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + chr_dir = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes" + chr_length = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Length/GRCm38.len" + dbsnp = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz" + dbsnp_tbi = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi" + dict = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict" + fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" + fasta_fai = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai" + intervals = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed" + known_indels = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz" + known_indels_tbi = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi" + mappability = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem" + readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" + snpeff_db = 'GRCm38.99' + vep_cache_version = '102' + vep_genome = 'GRCm38' + vep_species = 'mus_musculus' } 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" + fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" } 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" + fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" } 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" + fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" } 'WBcel235' { - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - snpeff_db = 'WBcel235.99' - vep_cache_version = '104' - vep_genome = 'WBcel235' - vep_species = 'caenorhabditis_elegans' + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" + snpeff_db = 'WBcel235.99' + vep_cache_version = '104' + vep_genome = 'WBcel235' + vep_species = 'caenorhabditis_elegans' } 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" + fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" } 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" + fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" } 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" + fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" } 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" + fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" } 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" + fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" } 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" + fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" } 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" + fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" } 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" + fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" } 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" + fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" } 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" } 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" + fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" } 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" + fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" } 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" + fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" } 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" + fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" } 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" + fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" } 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" + fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" } 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" } 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" + fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" } 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" + fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}" + readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" } } } diff --git a/main.nf b/main.nf index 6287617b83..8e6e3df37c 100644 --- a/main.nf +++ b/main.nf @@ -34,26 +34,26 @@ nextflow.enable.dsl = 2 ======================================================================================== */ -params.ac_loci = WorkflowMain.getGenomeAttribute(params, 'ac_loci') -params.ac_loci_gc = WorkflowMain.getGenomeAttribute(params, 'ac_loci_gc') -params.bwa = WorkflowMain.getGenomeAttribute(params, 'bwa') -params.chr_dir = WorkflowMain.getGenomeAttribute(params, 'chr_dir') -params.chr_length = WorkflowMain.getGenomeAttribute(params, 'chr_length') -params.dbsnp = WorkflowMain.getGenomeAttribute(params, 'dbsnp') -params.dbsnp_index = WorkflowMain.getGenomeAttribute(params, 'dbsnp_index') -params.dict = WorkflowMain.getGenomeAttribute(params, 'dict') -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_index = WorkflowMain.getGenomeAttribute(params, 'germline_resource_index') -params.intervals = WorkflowMain.getGenomeAttribute(params, 'intervals') -params.known_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels') -params.known_indels_index = WorkflowMain.getGenomeAttribute(params, 'known_indels_index') -params.mappability = WorkflowMain.getGenomeAttribute(params, 'mappability') -params.snpeff_db = WorkflowMain.getGenomeAttribute(params, 'snpeff_db') -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.ac_loci = WorkflowMain.getGenomeAttribute(params, 'ac_loci') +params.ac_loci_gc = WorkflowMain.getGenomeAttribute(params, 'ac_loci_gc') +params.bwa = WorkflowMain.getGenomeAttribute(params, 'bwa') +params.chr_dir = WorkflowMain.getGenomeAttribute(params, 'chr_dir') +params.chr_length = WorkflowMain.getGenomeAttribute(params, 'chr_length') +params.dbsnp = WorkflowMain.getGenomeAttribute(params, 'dbsnp') +params.dbsnp_tbi = WorkflowMain.getGenomeAttribute(params, 'dbsnp_tbi') +params.dict = WorkflowMain.getGenomeAttribute(params, 'dict') +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_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels') +params.known_indels_tbi = WorkflowMain.getGenomeAttribute(params, 'known_indels_tbi') +params.mappability = WorkflowMain.getGenomeAttribute(params, 'mappability') +params.snpeff_db = WorkflowMain.getGenomeAttribute(params, 'snpeff_db') +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') /* ======================================================================================== diff --git a/nextflow.config b/nextflow.config index 4192432e55..a09280320f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -58,7 +58,7 @@ params { generate_gvcf = null // g.vcf are not produced by HaplotypeCaller by default no_strelka_bp = null // Strelka will use Manta candidateSmallIndels if available pon = false // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope - pon_index = false // No default PON index for GATK Mutect2 / Sentieon TNscope + pon_tbi = false // No default PON index for GATK Mutect2 / Sentieon TNscope ignore_soft_clipped_bases = null // no --dont-use-soft-clipped-bases for GATK Mutect2 umi = null // no umi read_structure1 = null // no umi diff --git a/nextflow_schema.json b/nextflow_schema.json index ca5bc7cdd5..3a95526ae3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -73,7 +73,7 @@ "fa_icon": "fas fa-clock", "description": "Estimate interval size.", "help_text": "Intervals are part of the genome chopped up, used to speed up preprocessing and variant calling", - "default": 1000 + "default": 1000.0 }, "sentieon": { "type": "boolean", @@ -278,7 +278,7 @@ "description": "Panel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope", "help_text": "Without PON, there will be no calls with PASS in the INFO field, only an unfiltered VCF is written.\nIt is recommended to make your own PON, as it depends on sequencer and library preparation.\nFor tests in iGenomes there is a dummy PON file in the Annotation/GermlineResource directory, but it should not be used as a real PON file.\n\nSee [PON documentation](https://gatk.broadinstitute.org/hc/en-us/articles/360042479112-CreateSomaticPanelOfNormals-BETA)\n> **NB** PON file should be bgzipped." }, - "pon_index": { + "pon_tbi": { "type": "string", "fa_icon": "fas fa-file", "description": "Index of PON panel-of-normals VCF", @@ -427,7 +427,7 @@ "fa_icon": "fas fa-file", "description": "Path to dbsnp file." }, - "dbsnp_index": { + "dbsnp_tbi": { "type": "string", "fa_icon": "fas fa-file", "description": "Path to dbsnp index.", @@ -460,7 +460,7 @@ "description": "Path to GATK Mutect2 Germline Resource File", "help_text": "The germline resource VCF file (bgzipped and tabixed) needed by GATK4 Mutect2 is a collection of calls that are likely present in the sample, with allele frequencies.\nThe AF info field must be present.\nYou can find a smaller, stripped gnomAD VCF file (most of the annotation is removed and only calls signed by PASS are stored) in the AWS iGenomes Annotation/GermlineResource folder." }, - "germline_resource_index": { + "germline_resource_tbi": { "type": "string", "fa_icon": "fas fa-file", "description": "Path to GATK Mutect2 Germline Resource Index", @@ -477,7 +477,7 @@ "fa_icon": "fas fa-copy", "description": "Path to known indels file" }, - "known_indels_index": { + "known_indels_tbi": { "type": "string", "fa_icon": "fas fa-copy", "description": "Path to known indels file index", @@ -777,4 +777,4 @@ "$ref": "#/definitions/generic_options" } ] -} +} \ No newline at end of file diff --git a/subworkflows/local/build_indices.nf b/subworkflows/local/build_indices.nf index 6ebb52a0f1..0ab42d8c46 100644 --- a/subworkflows/local/build_indices.nf +++ b/subworkflows/local/build_indices.nf @@ -65,26 +65,34 @@ workflow BUILD_INDICES { result_dbsnp_tbi = Channel.empty() version_dbsnp_tbi = Channel.empty() - if (!(params.dbsnp_index) && params.dbsnp && ('mapping' in step || 'prepare_recalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) - (result_dbsnp_tbi, version_dbsnp_tbi) = TABIX_DBSNP([[id:"${dbsnp.baseName}"], dbsnp]) - result_dbsnp_tbi = result_dbsnp_tbi.map {meta, tbi -> [tbi]} + if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'prepare_recalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { + dbsnp_id = dbsnp.map {it -> [[id:"$it.baseName"], it]} + (result_dbsnp_tbi, version_dbsnp_tbi) = TABIX_DBSNP(dbsnp_id) + result_dbsnp_tbi = result_dbsnp_tbi.map {meta, tbi -> [tbi]} + } result_target_bed = Channel.empty() version_target_bed = Channel.empty() - if ((params.target_bed) && ('manta' in tools || 'strelka' in tools)) - (result_target_bed, version_target_bed) = TABIX_BGZIPTABIX([[id:"${target_bed.fileName}"], target_bed]) + if ((params.target_bed) && ('manta' in tools || 'strelka' in tools)) { + target_bed_id = target_bed.map {it -> [[id:"$it.baseName"], it]} + (result_target_bed, version_target_bed) = TABIX_BGZIPTABIX(target_bed_id) result_target_bed = result_target_bed.map {meta, bed, tbi -> [bed, tbi]} + } result_germline_resource_tbi = Channel.empty() version_germline_resource_tbi = Channel.empty() - if (!(params.germline_resource_index) && params.germline_resource && 'mutect2' in tools) - (result_germline_resource_tbi, version_germline_resource_tbi) = TABIX_GERMLINE_RESOURCE([[id:"${germline_resource.baseName}"], germline_resource]) + if (!(params.germline_resource_tbi) && params.germline_resource && 'mutect2' in tools){ + germline_resource_id = germline_resource.map {it -> [[id:"$it.baseName"], it]} + (result_germline_resource_tbi, version_germline_resource_tbi) = TABIX_GERMLINE_RESOURCE(germline_resource_id) + } result_known_indels_tbi = Channel.empty() version_known_indels_tbi = Channel.empty() - if (!(params.known_indels_index) && params.known_indels && ('mapping' in step || 'prepare_recalibration' in step)) - (result_known_indels_tbi, version_known_indels_tbi) = TABIX_KNOWN_INDELS([[id:"${known_indels.baseName}"], known_indels]) - result_known_indels_tbi = result_known_indels_tbi.map {meta, tbi -> [tbi]} + if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'prepare_recalibration' in step)){ + known_indels_id = known_indels.map {it -> [[id:"$it.baseName"], it]} + (result_known_indels_tbi, version_known_indels_tbi) = TABIX_KNOWN_INDELS(known_indels_id) + result_known_indels_tbi = result_known_indels_tbi.map {meta, tbi -> [tbi]} + } result_msisensorpro_scan = Channel.empty() version_msisensorpro_scan = Channel.empty() @@ -93,8 +101,10 @@ workflow BUILD_INDICES { result_pon_tbi = Channel.empty() version_pon_tbi = Channel.empty() - if (!(params.pon_index) && params.pon && ('tnscope' in tools || 'mutect2' in tools)) - (result_pon_tbi, version_pon_tbi) = TABIX_PON([[id:"${pon.fileName}"], pon]) + if (!(params.pon_tbi) && params.pon && ('tnscope' in tools || 'mutect2' in tools)){ + pon_id = pon.map {it -> [[id:"$it.baseName"], it]} + (result_pon_tbi, version_pon_tbi) = TABIX_PON(pon_id) + } result_intervals = Channel.empty() if (params.no_intervals) { diff --git a/workflows/sarek.nf b/workflows/sarek.nf index fcf41b17f8..fb55963628 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -20,14 +20,18 @@ def checkPathParamList = [ params.chr_dir, params.chr_length, params.dbsnp, + params.dbsnp_tbi, params.fasta, params.fasta_fai, params.germline_resource, + params.germline_resource_tbi, params.input, params.known_indels, + params.known_indels_tbi, params.mappability, params.multiqc_config, params.pon, + params.pon_tbi, params.snpeff_cache, params.target_bed, params.vep_cache @@ -68,7 +72,7 @@ if (anno_readme && file(anno_readme).exists()) { } // Stage dummy file to be used as an optional input where required -ch_dummy_file = file("$projectDir/assets/dummy_file.txt", checkIfExists: true) +ch_dummy_file = Channel.fromPath("$projectDir/assets/dummy_file.txt", checkIfExists: true).collect() /* ======================================================================================== @@ -101,36 +105,40 @@ if (params.skip_markduplicates) { } // Initialize file channels based on params, defined in the params.genomes[params.genome] scope -chr_dir = params.chr_dir ? file(params.chr_dir) : ch_dummy_file -chr_length = params.chr_length ? file(params.chr_length) : ch_dummy_file -dbsnp = params.dbsnp ? file(params.dbsnp) : ch_dummy_file -fasta = params.fasta ? file(params.fasta) : ch_dummy_file -fasta_fai = params.fasta_fai ? file(params.fasta_fai) : ch_dummy_file -germline_resource = params.germline_resource ? file(params.germline_resource) : ch_dummy_file -known_indels = params.known_indels ? file(params.known_indels) : ch_dummy_file -loci = params.ac_loci ? file(params.ac_loci) : ch_dummy_file -loci_gc = params.ac_loci_gc ? file(params.ac_loci_gc) : ch_dummy_file -mappability = params.mappability ? file(params.mappability) : ch_dummy_file +chr_dir = params.chr_dir ? Channel.fromPath(params.chr_dir).collect() : ch_dummy_file +chr_length = params.chr_length ? Channel.fromPath(params.chr_length).collect() : ch_dummy_file +dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : ch_dummy_file +dbsnp_tbi = params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : ch_dummy_file +fasta = params.fasta ? Channel.fromPath(params.fasta).collect() : ch_dummy_file +fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : ch_dummy_file +germline_resource = params.germline_resource ? Channel.fromPath(params.germline_resource).collect() : ch_dummy_file +germline_resource_tbi = params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi).collect() : ch_dummy_file +known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : ch_dummy_file +known_indels_tbi = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : ch_dummy_file +loci = params.ac_loci ? Channel.fromPath(params.ac_loci).collect() : ch_dummy_file +loci_gc = params.ac_loci_gc ? Channel.fromPath(params.ac_loci_gc).collect() : ch_dummy_file +mappability = params.mappability ? Channel.fromPath(params.mappability).collect() : ch_dummy_file // Initialize value channels based on params, defined in the params.genomes[params.genome] scope -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() +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() // Initialize files channels based on params, not defined within the params.genomes[params.genome] scope -cadd_indels = params.cadd_indels ? file(params.cadd_indels) : ch_dummy_file -cadd_indels_tbi = params.cadd_indels_tbi ? file(params.cadd_indels_tbi) : ch_dummy_file -cadd_wg_snvs = params.cadd_wg_snvs ? file(params.cadd_wg_snvs) : ch_dummy_file -cadd_wg_snvs_tbi = params.cadd_wg_snvs_tbi ? file(params.cadd_wg_snvs_tbi) : ch_dummy_file -pon = params.pon ? file(params.pon) : ch_dummy_file -snpeff_cache = params.snpeff_cache ? file(params.snpeff_cache) : ch_dummy_file -target_bed = params.target_bed ? file(params.target_bed) : ch_dummy_file -vep_cache = params.vep_cache ? file(params.vep_cache) : ch_dummy_file +cadd_indels = params.cadd_indels ? Channel.fromPath(params.cadd_indels).collect() : ch_dummy_file +cadd_indels_tbi = params.cadd_indels_tbi ? Channel.fromPath(params.cadd_indels_tbi).collect() : ch_dummy_file +cadd_wg_snvs = params.cadd_wg_snvs ? Channel.fromPath(params.cadd_wg_snvs).collect() : ch_dummy_file +cadd_wg_snvs_tbi = params.cadd_wg_snvs_tbi ? Channel.fromPath(params.cadd_wg_snvs_tbi).collect() : ch_dummy_file +pon = params.pon ? Channel.fromPath(params.pon).collect() : ch_dummy_file +pon_tbi = params.pon_tbi ? Channel.fromPath(params.pon_tbi).collect() : ch_dummy_file +snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : ch_dummy_file +target_bed = params.target_bed ? Channel.fromPath(params.target_bed).collect() : ch_dummy_file +vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : ch_dummy_file // Initialize value channels based on params, not defined within the params.genomes[params.genome] scope -read_structure1 = params.read_structure1 ?: Channel.empty() -read_structure2 = params.read_structure2 ?: Channel.empty() +read_structure1 = params.read_structure1 ?: Channel.empty() +read_structure2 = params.read_structure2 ?: Channel.empty() /* ======================================================================================== @@ -139,51 +147,50 @@ read_structure2 = params.read_structure2 ?: Channel.empty() */ include { BUILD_INDICES } from '../subworkflows/local/build_indices' addParams( - bgziptabix_target_bed_options: modules['bgziptabix_target_bed'], - build_intervals_options: modules['build_intervals'], - bwa_index_options: modules['bwa_index'], - bwamem2_index_options: modules['bwamem2_index'], - create_intervals_bed_options: modules['create_intervals_bed'], - gatk4_dict_options: modules['dict'], - msisensorpro_scan_options: modules['msisensorpro_scan'], - samtools_faidx_options: modules['samtools_faidx'], - tabix_dbsnp_options: modules['tabix_dbsnp'], - tabix_germline_resource_options: modules['tabix_germline_resource'], - tabix_known_indels_options: modules['tabix_known_indels'], - tabix_pon_options: modules['tabix_pon'] + bgziptabix_target_bed_options: modules['bgziptabix_target_bed'], + build_intervals_options: modules['build_intervals'], + bwa_index_options: modules['bwa_index'], + bwamem2_index_options: modules['bwamem2_index'], + create_intervals_bed_options: modules['create_intervals_bed'], + gatk4_dict_options: modules['dict'], + msisensorpro_scan_options: modules['msisensorpro_scan'], + samtools_faidx_options: modules['samtools_faidx'], + tabix_dbsnp_options: modules['tabix_dbsnp'], + tabix_germline_resource_options: modules['tabix_germline_resource'], + tabix_known_indels_options: modules['tabix_known_indels'], + tabix_pon_options: modules['tabix_pon'] ) include { MAPPING } from '../subworkflows/nf-core/mapping' addParams( - seqkit_split2_options: modules['seqkit_split2'], - bwamem1_mem_options: modules['bwa_mem1_mem'], - bwamem1_mem_tumor_options: modules['bwa_mem1_mem_tumor'], - bwamem2_mem_options: modules['bwa_mem2_mem'], - bwamem2_mem_tumor_options: modules['bwa_mem2_mem_tumor'], + bwamem1_mem_options: modules['bwa_mem1_mem'], + bwamem1_mem_tumor_options: modules['bwa_mem1_mem_tumor'], + bwamem2_mem_options: modules['bwa_mem2_mem'], + bwamem2_mem_tumor_options: modules['bwa_mem2_mem_tumor'], + seqkit_split2_options: modules['seqkit_split2'] ) include { QC_MARKDUPLICATES } from '../subworkflows/nf-core/qc_markduplicates' addParams( - markduplicates_options: modules['markduplicates'], - markduplicatesspark_options: modules['markduplicatesspark'], - estimatelibrarycomplexity_options: modules['estimatelibrarycomplexity'], - merge_bam_options: modules['merge_bam_mapping'], - qualimap_bamqc_options: modules['qualimap_bamqc_mapping'], - samtools_stats_options: modules['samtools_stats_mapping'], - samtools_view_options: modules['samtools_view'], - samtools_index_options: modules['samtools_index_cram'] + estimatelibrarycomplexity_options: modules['estimatelibrarycomplexity'], + markduplicates_options: modules['markduplicates'], + markduplicatesspark_options: modules['markduplicatesspark'], + merge_bam_options: modules['merge_bam_mapping'], + qualimap_bamqc_options: modules['qualimap_bamqc_mapping'], + samtools_index_options: modules['samtools_index_cram'], + samtools_stats_options: modules['samtools_stats_mapping'], + samtools_view_options: modules['samtools_view'] ) - include { PREPARE_RECALIBRATION } from '../subworkflows/nf-core/prepare_recalibration' addParams( - baserecalibrator_options: modules['baserecalibrator'], - baserecalibrator_spark_options: modules['baserecalibrator_spark'], - gatherbqsrreports_options: modules['gatherbqsrreports'] + baserecalibrator_options: modules['baserecalibrator'], + baserecalibrator_spark_options: modules['baserecalibrator_spark'], + gatherbqsrreports_options: modules['gatherbqsrreports'] ) include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' addParams( - applybqsr_options: modules['applybqsr'], - applybqsr_spark_options: modules['applybqsr_spark'], - merge_cram_options: modules['merge_cram_recalibrate'], - qualimap_bamqc_options: modules['qualimap_bamqc_recalibrate'], - samtools_index_options: modules['samtools_index_recalibrate'], - samtools_stats_options: modules['samtools_stats_recalibrate'] + applybqsr_options: modules['applybqsr'], + applybqsr_spark_options: modules['applybqsr_spark'], + merge_cram_options: modules['merge_cram_recalibrate'], + qualimap_bamqc_options: modules['qualimap_bamqc_recalibrate'], + samtools_index_options: modules['samtools_index_recalibrate'], + samtools_stats_options: modules['samtools_stats_recalibrate'] ) include { MAPPING_CSV } from '../subworkflows/local/mapping_csv' include { MARKDUPLICATES_CSV } from '../subworkflows/local/markduplicates_csv' @@ -273,17 +280,13 @@ workflow SAREK { dict = params.dict ? file(params.dict) : BUILD_INDICES.out.dict fai = params.fasta_fai ? file(params.fasta_fai) : BUILD_INDICES.out.fai - dbsnp_tbi = params.dbsnp ? params.dbsnp_index ? Channel.fromPath(params.dbsnp_index) : BUILD_INDICES.out.dbsnp_tbi : [] - germline_resource_tbi = params.germline_resource ? params.germline_resource_index ? Channel.from(params.germline_resource_index) : BUILD_INDICES.out.germline_resource_tbi : [] - known_indels_tbi = params.known_indels ? params.known_indels_index ? Channel.fromPath(params.known_indels_index) : BUILD_INDICES.out.known_indels_tbi.collect() : [] - pon_tbi = params.pon ? params.pon_index ? Channel.from(params.pon_index) : BUILD_INDICES.out.pon_tbi : [] - - dbsnp_ch = Channel.from(dbsnp) - dbsnp_tbi_ch = Channel.from(dbsnp_tbi) - known_indels_ch = Channel.from(known_indels) + dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi) : BUILD_INDICES.out.dbsnp_tbi : [] + germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi) : BUILD_INDICES.out.germline_resource_tbi : [] + known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi) : BUILD_INDICES.out.known_indels_tbi.collect() : [] + pon_tbi = params.pon ? params.pon_tbi ? Channel.fromPath(params.pon_tbi) : BUILD_INDICES.out.pon_tbi : [] //TODO @Rike, is this working for you? - known_sites = dbsnp ? [dbsnp, known_indels] : known_indels ? known_indels : [] + known_sites = dbsnp ? dbsnp.concat(known_indels).collect() : ch_dummy_file known_sites_tbi = dbsnp_tbi ? dbsnp_tbi.concat(known_indels_tbi).collect() : ch_dummy_file msisensorpro_scan = BUILD_INDICES.out.msisensorpro_scan