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maxulyssemaxulysse
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add iGenomes specific config
1 parent 347bebb commit 6ce9d62

5 files changed

Lines changed: 68 additions & 30 deletions

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‎conf/aws-batch.config‎

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@@ -8,7 +8,7 @@
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*/
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params {
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genome_base = params.genome == 'iGRCh37' ? "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37" : params.genome == 'iGRCh38' ? "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38" : "s3://sarek-references/small"
11+
genome_base = params.genome == 'GRCh37' ? "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37" : params.genome == 'GRCh38' ? "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38" : "s3://sarek-references/small"
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publishDirMode = 'copy'
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}
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‎conf/base.config‎

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@@ -6,7 +6,6 @@
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* -------------------------------------------------
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*/
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includeConfig 'genomes.config'
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wf_repository = 'maxulysse'
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params {

‎conf/genomes.config‎

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@@ -42,32 +42,6 @@ params {
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//AF_files = "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf"
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//AF_indexes = "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf.idx"
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}
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'iGRCh37' {
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acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
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dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf"
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dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
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genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
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genomeDict = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
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genomeIndex = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
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bwaIndex = "${params.genome_base}/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
53-
intervals = "${params.genome_base}/Annotation/intervals/wgs_calling_regions_CAW.list"
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knownIndels = "${params.genome_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
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knownIndelsIndex = "${params.genome_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
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snpeffDb = "GRCh37.75"
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}
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'iGRCh38' {
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acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
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dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
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dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
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genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
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genomeDict = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
64-
genomeIndex = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
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bwaIndex = "${params.genome_base}/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
66-
intervals = "${params.genome_base}/Annotation/intervals/wgs_calling_regions.hg38.bed"
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knownIndels = "${params.genome_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
68-
knownIndelsIndex = "${params.genome_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
69-
snpeffDb = "GRCh38.86"
70-
}
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'smallGRCh37' {
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acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
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dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf"

‎conf/igenomes.config‎

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@@ -0,0 +1,56 @@
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/*
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* -------------------------------------------------
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* Nextflow config file for Sarek
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* -------------------------------------------------
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* Path to reference files
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* -------------------------------------------------
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* Imported under all Nextflow profiles in
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* nextflow.config
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* -------------------------------------------------
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* Modify to add specific versions of genomes
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* -------------------------------------------------
12+
*/
13+
14+
params {
15+
genomes {
16+
'GRCh37' {
17+
acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
18+
dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf"
19+
dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
20+
genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
21+
genomeDict = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
22+
genomeIndex = "${params.genome_base}/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
23+
bwaIndex = "${params.genome_base}/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
24+
intervals = "${params.genome_base}/Annotation/intervals/wgs_calling_regions_CAW.list"
25+
knownIndels = "${params.genome_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
26+
knownIndelsIndex = "${params.genome_base}/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
27+
snpeffDb = "GRCh37.75"
28+
}
29+
'GRCh38' {
30+
acLoci = "${params.genome_base}/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
31+
dbsnp = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
32+
dbsnpIndex = "${params.genome_base}/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
33+
genomeFile = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
34+
genomeDict = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
35+
genomeIndex = "${params.genome_base}/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
36+
bwaIndex = "${params.genome_base}/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
37+
intervals = "${params.genome_base}/Annotation/intervals/wgs_calling_regions.hg38.bed"
38+
knownIndels = "${params.genome_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
39+
knownIndelsIndex = "${params.genome_base}/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
40+
snpeffDb = "GRCh38.86"
41+
}
42+
'smallGRCh37' {
43+
acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
44+
dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf"
45+
dbsnpIndex = "${dbsnp}.idx"
46+
genomeFile = "${params.genome_base}/human_g1k_v37_decoy.small.fasta"
47+
bwaIndex = "${genomeFile}.{amb,ann,bwt,pac,sa}"
48+
genomeDict = "${params.genome_base}/human_g1k_v37_decoy.small.dict"
49+
genomeIndex = "${genomeFile}.fai"
50+
intervals = "${params.genome_base}/small.intervals"
51+
knownIndels = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf"
52+
knownIndelsIndex = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf.idx"
53+
snpeffDb = "GRCh37.75"
54+
}
55+
}
56+
}

‎nextflow.config‎

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@@ -28,6 +28,7 @@ profiles {
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// Singularity images need to be set up
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standard {
3030
includeConfig 'conf/base.config'
31+
includeConfig 'conf/genomes.config'
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includeConfig 'conf/uppmax-localhost.config'
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includeConfig 'conf/singularity-path.config'
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}
@@ -36,6 +37,7 @@ profiles {
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// Singularity images need to be set up
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slurm {
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includeConfig 'conf/base.config'
40+
includeConfig 'conf/genomes.config'
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includeConfig 'conf/uppmax-slurm.config'
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includeConfig 'conf/singularity-path.config'
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}
@@ -44,6 +46,7 @@ profiles {
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// Singularity images will be pulled automatically
4547
slurmDownload {
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includeConfig 'conf/base.config'
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includeConfig 'conf/genomes.config'
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includeConfig 'conf/uppmax-slurm.config'
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includeConfig 'conf/singularity.config'
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includeConfig 'conf/containers.config'
@@ -52,6 +55,7 @@ profiles {
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// Docker images will be pulled automatically
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docker {
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includeConfig 'conf/base.config'
58+
includeConfig 'conf/genomes.config'
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includeConfig 'conf/travis.config'
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includeConfig 'conf/docker.config'
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includeConfig 'conf/containers.config'
@@ -60,6 +64,7 @@ profiles {
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// Docker images will be pulled automatically
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awsbatch {
6266
includeConfig 'conf/base.config'
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includeConfig 'conf/igenomes.config'
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includeConfig 'conf/aws-batch.config'
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includeConfig 'conf/docker.config'
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includeConfig 'conf/containers.config'
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// Singularity images will be pulled automatically
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singularity {
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includeConfig 'conf/base.config'
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includeConfig 'conf/genomes.config'
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includeConfig 'conf/travis.config'
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includeConfig 'conf/singularity.config'
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includeConfig 'conf/containers.config'
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// Singularity images need to be set up
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singularityPath {
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includeConfig 'conf/base.config'
85+
includeConfig 'conf/genomes.config'
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includeConfig 'conf/travis.config'
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includeConfig 'conf/singularity-path.config'
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}
@@ -85,14 +92,16 @@ profiles {
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// Singularity images will be pulled automatically
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binac {
8794
includeConfig 'conf/base.config'
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includeConfig 'conf/genomes.config'
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includeConfig 'conf/binac.config'
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includeConfig 'conf/singularity.config'
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includeConfig 'conf/resources.config'
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includeConfig 'conf/containers.config'
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}
93-
// Default config for CFC cluster in Tuebingen/Germany
101+
// Default config for CFC cluster in Tuebingen/Germany
94102
cfc {
95103
includeConfig 'conf/base.config'
104+
includeConfig 'conf/genomes.config'
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includeConfig 'conf/cfc.config'
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includeConfig 'conf/singularity.config'
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includeConfig 'conf/resources.config'
@@ -132,4 +141,4 @@ def check_max(obj, type) {
132141
return obj
133142
}
134143
}
135-
}
144+
}

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