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fix annotation tests #143

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merged 6 commits into from
Mar 5, 2020
Merged

fix annotation tests #143

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8a90d47
fix annotation tests
maxulysse Mar 5, 2020
2933c35
code polishing
maxulysse Mar 5, 2020
c1c9470
use iGenomes
maxulysse Mar 5, 2020
92748ed
reorganise configs
maxulysse Mar 5, 2020
cb5b704
update CHANGELOG
maxulysse Mar 5, 2020
456dd79
update databases
maxulysse Mar 5, 2020
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9 changes: 2 additions & 7 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ jobs:
- image: circleci/buildpack-deps:stretch
environment:
GENOME: GRCh37
SNPEFF_CACHE_VERSION: "87"
SNPEFF_CACHE_VERSION: "75"
steps:
- checkout
- setup_remote_docker
Expand All @@ -20,7 +20,7 @@ jobs:
<< : *buildsnpeff
environment:
GENOME: GRCh38
SNPEFF_CACHE_VERSION: "92"
SNPEFF_CACHE_VERSION: "86"

snpeffgrcm38:
<< : *buildsnpeff
Expand Down Expand Up @@ -60,29 +60,24 @@ jobs:
<< : *buildvep
environment:
GENOME: GRCh38
SPECIES: homo_sapiens
VEP_VERSION: "99"

vepgrcm38:
<< : *buildvep
environment:
GENOME: GRCm38
SPECIES: mus_musculus
VEP_VERSION: "99"

vepcanfam3_1:
<< : *buildvep
environment:
GENOME: CanFam3.1
SPECIES: canis_familiaris
VEP_VERSION: "99"

vepwbcel235:
<< : *buildvep
environment:
GENOME: WBcel235
SPECIES: caenorhabditis_elegans
VEP_VERSION: "99"

workflows:
version: 2
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -32,7 +32,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
tools: [snpeff, VEP]
tools: [snpeff, vep]
species: [WBcel235]
steps:
- uses: actions/checkout@v2
Expand Down
3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -37,6 +37,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version to `87` for `GRCh37`
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `snpEff` cache version to `92` for `GRCh38`
- [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37`
- [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38`

### `Fixed`

Expand All @@ -50,6 +52,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
- [#129](https://github.com/nf-core/sarek/pull/129) - Removed `Python` `3.7.3` from conda environment due to incompatibility
- [#129](https://github.com/nf-core/sarek/pull/129) - Change ascii characters that were not supported from the `output.md` docs
- [#141](https://github.com/nf-core/sarek/pull/141) - Fix `download_cache.nf` script to download cache for `snpEff` and `VEP`
- [#143](https://github.com/nf-core/sarek/pull/143) - Fix annotation CI testing with `snpEff` and `VEP`

### `Deprecated`

Expand Down
9 changes: 7 additions & 2 deletions conf/genomes.config
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Expand Up @@ -25,7 +25,7 @@ params {
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 = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
snpeff_db = 'GRCh37.87'
snpeff_db = 'GRCh37.75'
species = 'homo_sapiens'
vep_cache_version = '99'
}
Expand All @@ -45,7 +45,7 @@ params {
intervals = "${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"
snpeff_db = 'GRCh38.92'
snpeff_db = 'GRCh38.86'
species = 'homo_sapiens'
vep_cache_version = '99'
}
Expand All @@ -66,5 +66,10 @@ params {
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
known_indels = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
}
'WBcel235' {
snpeff_db = 'WBcel235.86'
species = 'caenorhabditis_elegans'
vep_cache_version = '99'
}
}
}
7 changes: 5 additions & 2 deletions conf/igenomes.config
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Expand Up @@ -25,7 +25,7 @@ params {
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 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
snpeff_db = 'GRCh37.87'
snpeff_db = 'GRCh37.75'
species = 'homo_sapiens'
vep_cache_version = '99'
}
Expand All @@ -45,7 +45,7 @@ params {
intervals = "${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"
snpeff_db = 'GRCh38.92'
snpeff_db = 'GRCh38.86'
species = 'homo_sapiens'
vep_cache_version = '99'
}
Expand Down Expand Up @@ -84,6 +84,9 @@ params {
'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 = 'WBcel235.86'
species = 'caenorhabditis_elegans'
vep_cache_version = '99'
}
'ce10' {
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
Expand Down
5 changes: 1 addition & 4 deletions conf/test_annotation.config
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Expand Up @@ -10,9 +10,6 @@
includeConfig 'test.config'

params {
input = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
genome = 'WBcel235'
species = 'caenorhabditis_elegans'
vep_cache_version = '99'
snpeff_db = 'WBcel235.86'
input = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/vcf/Strelka_1234N_variants.vcf.gz'
}
2 changes: 0 additions & 2 deletions main.nf
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Expand Up @@ -418,8 +418,6 @@ if (tsvPath) {

(genderMap, statusMap, inputSample) = extractInfos(inputSample)



/*
================================================================================
CHECKING REFERENCES
Expand Down