This repository has been archived by the owner on Jan 27, 2020. It is now read-only.
forked from nf-core/sarek
-
Notifications
You must be signed in to change notification settings - Fork 6
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #697 from MaxUlysse/iGenomes
iGenomes specific config file
- Loading branch information
Showing
7 changed files
with
94 additions
and
42 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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" | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters