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Merge pull request #697 from MaxUlysse/iGenomes
iGenomes specific config file
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| /* | ||
| * ------------------------------------------------- | ||
| * Nextflow config file for Sarek | ||
| * ------------------------------------------------- | ||
| * Path to iGenomes reference files | ||
| * ------------------------------------------------- | ||
| * Imported under Nextflow profiles in | ||
| * nextflow.config | ||
| * ------------------------------------------------- | ||
| * Defines reference genomes, using iGenome paths | ||
| * Can be used by any config that customises the base | ||
| * path using $params.genome_base / --genome_base | ||
| * ------------------------------------------------- | ||
| */ | ||
|
|
||
| params { | ||
| genomes { | ||
| 'GRCh37' { | ||
| acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci" | ||
| dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf" | ||
| dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx" | ||
| genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta" | ||
| genomeDict = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict" | ||
| genomeIndex = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai" | ||
| bwaIndex = "${params.genome_base}/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}" | ||
| intervals = "${params.genome_base}/Annotation/intervals/wgs_calling_regions_CAW.list" | ||
| knownIndels = "${params.genome_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf" | ||
| knownIndelsIndex = "${params.genome_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx" | ||
| snpeffDb = "GRCh37.75" | ||
| } | ||
| 'GRCh38' { | ||
| acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci" | ||
| dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz" | ||
| dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi" | ||
| genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta" | ||
| genomeDict = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict" | ||
| genomeIndex = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai" | ||
| bwaIndex = "${params.genome_base}/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}" | ||
| intervals = "${params.genome_base}/Annotation/intervals/wgs_calling_regions.hg38.bed" | ||
| knownIndels = "${params.genome_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz" | ||
| knownIndelsIndex = "${params.genome_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi" | ||
| snpeffDb = "GRCh38.86" | ||
| } | ||
| 'smallGRCh37' { | ||
| acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci" | ||
| dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf" | ||
| dbsnpIndex = "${dbsnp}.idx" | ||
| genomeFile = "${params.genome_base}/human_g1k_v37_decoy.small.fasta" | ||
| bwaIndex = "${genomeFile}.{amb,ann,bwt,pac,sa}" | ||
| genomeDict = "${params.genome_base}/human_g1k_v37_decoy.small.dict" | ||
| genomeIndex = "${genomeFile}.fai" | ||
| intervals = "${params.genome_base}/small.intervals" | ||
| knownIndels = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf" | ||
| knownIndelsIndex = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf.idx" | ||
| snpeffDb = "GRCh37.75" | ||
| } | ||
| } | ||
| } |
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