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FEAT: Use annotation-cache and update VEP to v110 #1122

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merged 24 commits into from
Aug 17, 2023
Merged

FEAT: Use annotation-cache and update VEP to v110 #1122

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34a59bb
use s3://annotation-cache
maxulysse Jun 20, 2023
690922e
sort list
maxulysse Jun 20, 2023
6ce0619
sort list
maxulysse Jun 20, 2023
971c850
add error message
maxulysse Jun 20, 2023
2fc8a85
update config files
maxulysse Jun 20, 2023
7462df1
remove container with built-in cache
maxulysse Jun 20, 2023
ef5efe2
update tests
maxulysse Jun 20, 2023
be19c48
remove snpeff_version and vep_version
maxulysse Jun 21, 2023
e9c73e0
rework meta.id key for VEP download
maxulysse Jun 21, 2023
7183f33
add use_annotation_cache_keys
maxulysse Jun 21, 2023
7f506f2
it's a params
maxulysse Jun 21, 2023
28f76e1
no need for /
maxulysse Jun 21, 2023
1aef254
update vep cache version
maxulysse Jun 22, 2023
afd0df5
Merge branch 'dev' of github.com:nf-core/sarek into annotation_cache
maxulysse Jul 6, 2023
0078a67
Merge branch 'dev' into annotation_cache
maxulysse Jul 9, 2023
a86340f
Merge branch 'dev' into annotation_cache
maxulysse Jul 13, 2023
e78b35a
Merge branch 'dev' into annotation_cache
maxulysse Jul 21, 2023
ef4e2ea
Update nextflow.config
maxulysse Jul 21, 2023
1fe7b55
update modules
maxulysse Jul 25, 2023
aa69d6b
fix meta maps
maxulysse Jul 26, 2023
2e77a5c
fix syntac
maxulysse Aug 16, 2023
29c323e
Merge branch 'dev' into annotation_cache
maxulysse Aug 17, 2023
cd72227
Apply suggestions from code review
maxulysse Aug 17, 2023
6ef8a46
update CHANGELOG
maxulysse Aug 17, 2023
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40 changes: 8 additions & 32 deletions conf/igenomes.config
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Original file line number Diff line number Diff line change
Expand Up @@ -37,11 +37,9 @@ params {
mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
snpeff_db = 87
snpeff_genome = 'GRCh37'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_version = '108.2'
}
'GATK.GRCh38' {
ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip"
Expand Down Expand Up @@ -74,34 +72,28 @@ params {
pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
snpeff_db = 105
snpeff_genome = 'GRCh38'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_version = '108.2'
}
'Ensembl.GRCh37' {
bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
snpeff_db = 87
snpeff_genome = 'GRCh37'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_version = '108.2'
}
'NCBI.GRCh38' {
bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 105
snpeff_genome = 'GRCh38'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_version = '108.2'
}
'CHM13' {
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
Expand All @@ -123,11 +115,9 @@ params {
readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
snpeff_db = 99
snpeff_genome = 'GRCm38'
snpeff_version = '5.1'
vep_cache_version = 102
vep_genome = 'GRCm38'
vep_species = 'mus_musculus'
vep_version = '108.2'
}
'TAIR10' {
bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
Expand All @@ -145,34 +135,28 @@ params {
readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
snpeff_db = 75
snpeff_genome = 'UMD3.1'
snpeff_version = '5.1'
vep_cache_version = 94
vep_genome = 'UMD3.1'
vep_species = 'bos_taurus'
vep_version = '108.2'
}
'WBcel235' {
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 105
snpeff_genome = 'WBcel235'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
vep_version = '108.2'
}
'CanFam3.1' {
bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
snpeff_db = 99
snpeff_genome = 'CanFam3.1'
snpeff_version = '5.1'
vep_cache_version = 104
vep_genome = 'CanFam3.1'
vep_species = 'canis_lupus_familiaris'
vep_version = '108.2'
}
'GRCz10' {
bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
Expand Down Expand Up @@ -228,11 +212,9 @@ params {
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 105
snpeff_genome = 'R64-1-1'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'R64-1-1'
vep_species = 'saccharomyces_cerevisiae'
vep_version = '108.2'
}
'EF2' {
bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
Expand All @@ -258,35 +240,29 @@ params {
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 105
snpeff_genome = 'GRCh38'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_version = '108.2'
}
'hg19' {
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
snpeff_db = 87
snpeff_genome = 'GRCh37'
snpeff_version = '5.1'
vep_cache_version = 108
vep_cache_version = 109
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_version = '108.2'
}
'mm10' {
bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
snpeff_db = 99
snpeff_genome = 'GRCm38'
snpeff_version = '5.1'
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vep_cache_version = 102
vep_genome = 'GRCm38'
vep_species = 'mus_musculus'
vep_version = '108.2'
}
'bosTau8' {
bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
Expand Down
2 changes: 0 additions & 2 deletions conf/modules/annotate.config
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@ process {
withName: 'SNPEFF_SNPEFF' {
ext.prefix = { vcf.baseName - ".vcf" + "_snpEff" }
ext.args = '-nodownload -canon -v'
if (!params.snpeff_cache && !params.download_cache) container = { params.snpeff_genome ? "docker.io/nfcore/snpeff:${params.snpeff_version}.${params.snpeff_genome}" : "docker.io/nfcore/snpeff:${params.snpeff_version}.${params.genome}" }
publishDir = [
[
mode: params.publish_dir_mode,
Expand All @@ -47,7 +46,6 @@ process {
].join(' ').trim() }
// If just VEP: <vcf prefix>_VEP.ann.vcf
ext.prefix = { vcf.baseName - ".vcf" + "_VEP.ann" }
if (!params.vep_cache && !params.download_cache) container = { params.vep_genome ? "docker.io/nfcore/vep:${params.vep_version}.${params.vep_genome}" : "docker.io/nfcore/vep:${params.vep_version}.${params.genome}" }
publishDir = [
[
mode: params.publish_dir_mode,
Expand Down
8 changes: 4 additions & 4 deletions conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -29,20 +29,20 @@ params {
germline_resource = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
intervals = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list"
known_indels = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
snpeff_cache = null
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snpeff_db = 105
snpeff_genome = 'WBcel235'
snpeff_version = '5.1'
vep_cache_version = 106
vep_cache = null
vep_cache_version = 108
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vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
vep_version = '106.1'

// default params
split_fastq = 0 // no FASTQ splitting
tools = 'strelka' // Variant calling with Strelka

// Ignore params that will throw warning through params validation
schema_ignore_params = 'genomes,snpeff_version,vep_version'
schema_ignore_params = 'genomes'
}

process {
Expand Down
8 changes: 4 additions & 4 deletions conf/test/cache.config
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Original file line number Diff line number Diff line change
Expand Up @@ -41,20 +41,20 @@ params {
germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz']
intervals = params.test_data['homo_sapiens']['genome']['genome_interval_list']
known_indels = params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz']
snpeff_cache = null
snpeff_db = 105
snpeff_genome = 'WBcel235'
snpeff_version = '5.1'
vep_cache_version = 106
vep_cache = null
vep_cache_version = 108
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vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
vep_version = '106.1'

// default params
split_fastq = 0 // no FASTQ splitting
tools = 'strelka' // Variant calling with Strelka

// Ignore params that will throw warning through params validation
schema_ignore_params = 'genomes,test_data,snpeff_version,vep_version'
schema_ignore_params = 'genomes,test_data'
}

process {
Expand Down
2 changes: 0 additions & 2 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -56,11 +56,9 @@ params.pon = WorkflowMain.getGenomeAttribute(params, 'pon')
params.pon_tbi = WorkflowMain.getGenomeAttribute(params, 'pon_tbi')
params.snpeff_db = WorkflowMain.getGenomeAttribute(params, 'snpeff_db')
params.snpeff_genome = WorkflowMain.getGenomeAttribute(params, 'snpeff_genome')
params.snpeff_version = WorkflowMain.getGenomeAttribute(params, 'snpeff_version')
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.vep_version = WorkflowMain.getGenomeAttribute(params, 'vep_version')

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down
4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -123,12 +123,12 @@
},
"ensemblvep/download": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "1b5ffd7aa6e3c21b702957c808cbd1c351dd1809",
"installed_by": ["modules"]
},
"ensemblvep/vep": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "1b5ffd7aa6e3c21b702957c808cbd1c351dd1809",
"installed_by": ["vcf_annotate_ensemblvep", "modules"]
},
"fastp": {
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/ensemblvep/download/main.nf
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8 changes: 5 additions & 3 deletions modules/nf-core/ensemblvep/download/meta.yml
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6 changes: 3 additions & 3 deletions modules/nf-core/ensemblvep/vep/main.nf
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39 changes: 20 additions & 19 deletions nextflow.config
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Expand Up @@ -71,24 +71,25 @@ params {
joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected

// Annotation
vep_out_format = 'vcf'
vep_custom_args = null // No custom arguments for VEP
vep_dbnsfp = null // dbnsfp plugin disabled within VEP
dbnsfp = null // No dbnsfp processed file
dbnsfp_tbi = null // No dbnsfp processed file index
dbnsfp_consequence = null // No default consequence for dbnsfp plugin
dbnsfp_fields = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
vep_loftee = null // loftee plugin disabled within VEP
vep_spliceai = null // spliceai plugin disabled within VEP
spliceai_snv = null // No spliceai_snv file
spliceai_snv_tbi = null // No spliceai_snv file index
spliceai_indel = null // No spliceai_indel file
spliceai_indel_tbi = null // No spliceai_indel file index
vep_spliceregion = null // spliceregion plugin disabled within VEP
outdir_cache = null // No output directory for cache
snpeff_cache = null // No directory for snpEff cache
vep_cache = null // No directory for VEP cache
vep_include_fasta = false // Don't use fasta file for annotation with VEP
outdir_cache = null // No output directory for cache
use_annotation_cache_keys = true
snpeff_cache = 's3://annotation-cache/snpeff_cache/'
vep_cache = 's3://annotation-cache/vep_cache/'
vep_custom_args = null // No custom arguments for VEP
vep_dbnsfp = null // dbnsfp plugin disabled within VEP
vep_include_fasta = false // Don't use fasta file for annotation with VEP
vep_loftee = null // loftee plugin disabled within VEP
vep_out_format = 'vcf'
vep_spliceai = null // spliceai plugin disabled within VEP
vep_spliceregion = null // spliceregion plugin disabled within VEP
dbnsfp = null // No dbnsfp processed file
dbnsfp_consequence = null // No default consequence for dbnsfp plugin
dbnsfp_fields = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
dbnsfp_tbi = null // No dbnsfp processed file index
spliceai_indel = null // No spliceai_indel file
spliceai_indel_tbi = null // No spliceai_indel file index
spliceai_snv = null // No spliceai_snv file
spliceai_snv_tbi = null // No spliceai_snv file index

// MultiQC options
multiqc_config = null
Expand All @@ -109,7 +110,7 @@ params {
version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,snpeff_version,vep_version,cf_ploidy'
schema_ignore_params = 'genomes,cf_ploidy'

// Config options
custom_config_version = 'master'
Expand Down
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