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Bump ensembl-vep modules to 110.0 #3658

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merged 14 commits into from
Jul 25, 2023
Merged

Bump ensembl-vep modules to 110.0 #3658

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299317e
bump ensembl-vep to 110.0
maxulysse Jul 21, 2023
58158b7
update tests
maxulysse Jul 21, 2023
71e5296
put conda tests back
maxulysse Jul 21, 2023
c4a2ec1
update config for ENSEMBLVEP_DOWNLOAD
maxulysse Jul 21, 2023
f9eb916
update tests for related subworkflows
maxulysse Jul 21, 2023
b084f2f
fix path to module
maxulysse Jul 21, 2023
c74828b
enable conda tests back
maxulysse Jul 21, 2023
10f8a37
better tests
maxulysse Jul 21, 2023
dd7127c
fix tests
maxulysse Jul 21, 2023
c3c3045
nicer channels
maxulysse Jul 21, 2023
19bd890
Merge branch 'master' into vep_110
maxulysse Jul 21, 2023
fec9d72
fix channel queue to value
maxulysse Jul 25, 2023
b5b545b
Merge branch 'master' into vep_110
maxulysse Jul 25, 2023
bb394ff
fix syntax
maxulysse Jul 25, 2023
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4 changes: 0 additions & 4 deletions .github/workflows/pytest-workflow.yml
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Expand Up @@ -76,8 +76,6 @@ jobs:
tags: deepcell/mesmer
- profile: "conda"
tags: deepvariant
- profile: "conda"
tags: ensemblvep/vep
- profile: "conda"
tags: fastk/fastk
- profile: "conda"
Expand Down Expand Up @@ -150,8 +148,6 @@ jobs:
tags: subworkflows/bcl_demultiplex
- profile: "conda"
tags: subworkflows/vcf_annotate_ensemblvep_snpeff
- profile: "conda"
tags: subworkflows/vcf_annotate_ensemblvep
- profile: "conda"
tags: subworkflows/fasta_clean_fcs
- profile: "conda"
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/ensemblvep/download/main.nf
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Expand Up @@ -2,10 +2,10 @@ process ENSEMBLVEP_DOWNLOAD {
tag "$meta.id"
label 'process_medium'

conda "bioconda::ensembl-vep=109.3"
conda "bioconda::ensembl-vep=110.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ensembl-vep:109.3--pl5321h2a3209d_1' :
'biocontainers/ensembl-vep:109.3--pl5321h2a3209d_1' }"
'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' :
'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }"

input:
tuple val(meta), val(assembly), val(species), val(cache_version)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/ensemblvep/vep/main.nf
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Expand Up @@ -2,10 +2,10 @@ process ENSEMBLVEP_VEP {
tag "$meta.id"
label 'process_medium'

conda "bioconda::ensembl-vep=109.3"
conda "bioconda::ensembl-vep=110.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ensembl-vep:109.3--pl5321h2a3209d_1' :
'biocontainers/ensembl-vep:109.3--pl5321h2a3209d_1' }"
'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' :
'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }"

input:
tuple val(meta), path(vcf), path(custom_extra_files)
Expand Down
11 changes: 7 additions & 4 deletions tests/modules/nf-core/ensemblvep/download/main.nf
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Expand Up @@ -2,10 +2,13 @@

nextflow.enable.dsl = 2

include { ENSEMBLVEP_DOWNLOAD } from '../../../../../modules/nf-core/ensemblvep/download/main.nf'
include { ENSEMBLVEP_DOWNLOAD } from '../../../../../modules/nf-core/ensemblvep/download/main'

workflow test_ensemblvep_download {
input = [[id:"test"], "WBcel235", "caenorhabditis_elegans", "108"]
vep_cache_version = "110"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
vep_cache_input = Channel.of([[id:"${vep_cache_version}_${vep_genome}"], vep_genome, vep_species, vep_cache_version])

ENSEMBLVEP_DOWNLOAD(input)
workflow test_ensemblvep_download {
ENSEMBLVEP_DOWNLOAD(vep_cache_input)
}
2 changes: 1 addition & 1 deletion tests/modules/nf-core/ensemblvep/download/test.yml
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Expand Up @@ -4,4 +4,4 @@
- ensemblvep
- ensemblvep/download
files:
- path: output/ensemblvep/vep_cache/caenorhabditis_elegans/108_WBcel235/
- path: output/ensemblvep/vep_cache/caenorhabditis_elegans/110_WBcel235/
142 changes: 90 additions & 52 deletions tests/modules/nf-core/ensemblvep/vep/main.nf
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Expand Up @@ -2,126 +2,164 @@

nextflow.enable.dsl = 2

include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_DEFAULT } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_JSON } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_TAB } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF_BGZIP } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF_GZIP } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_CUSTOM } from '../../../../../modules/nf-core/ensemblvep/vep/main.nf'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_DEFAULT } from '../../../../../modules/nf-core/ensemblvep/vep/main'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_JSON } from '../../../../../modules/nf-core/ensemblvep/vep/main'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_TAB } from '../../../../../modules/nf-core/ensemblvep/vep/main'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF } from '../../../../../modules/nf-core/ensemblvep/vep/main'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF_BGZIP } from '../../../../../modules/nf-core/ensemblvep/vep/main'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_VCF_GZIP } from '../../../../../modules/nf-core/ensemblvep/vep/main'
include { ENSEMBLVEP_VEP as ENSEMBLVEP_VEP_CUSTOM } from '../../../../../modules/nf-core/ensemblvep/vep/main'
include { ENSEMBLVEP_DOWNLOAD } from '../../../../../modules/nf-core/ensemblvep/download/main'

vep_cache_version = "110"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
vep_cache_input = Channel.of([[id:"${vep_cache_version}_${vep_genome}"], vep_genome, vep_species, vep_cache_version])

workflow test_ensemblvep_vep_fasta_json {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
]
])

fasta = [
[ id: 'fasta' ],
fasta = Channel.value([
[id:"fasta"],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
])

ENSEMBLVEP_VEP_JSON ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] )
ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

ENSEMBLVEP_VEP_JSON ( input, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, [] )
}

workflow test_ensemblvep_vep_fasta_tab {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
]
])

ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

fasta = [
[ id: 'fasta' ],
fasta = Channel.value([
[id:"fasta"],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
])

ENSEMBLVEP_VEP_TAB ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] )
ENSEMBLVEP_VEP_TAB ( input, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, [] )
}

workflow test_ensemblvep_vep_fasta_vcf {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
]
])

fasta = [
[ id: 'fasta' ],
fasta = Channel.value([
[id:"fasta"],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
])

ENSEMBLVEP_VEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] )
ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

ENSEMBLVEP_VEP_VCF ( input, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, [] )
}

workflow test_ensemblvep_vep_fasta_vcf_bgzip {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
]
])

fasta = [
[ id: 'fasta' ],
fasta = Channel.value([
[id:"fasta"],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
])

ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

ENSEMBLVEP_VEP_VCF_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] )
ENSEMBLVEP_VEP_VCF_BGZIP ( input, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, [] )
}

workflow test_ensemblvep_vep_fasta_vcf_gzip {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
]
])

fasta = [
[ id: 'fasta' ],
fasta = Channel.value([
[id:"fasta"],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
])

ENSEMBLVEP_VEP_VCF_GZIP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] )
ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

ENSEMBLVEP_VEP_VCF_GZIP ( input, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, [] )
}

workflow test_ensemblvep_vep_fasta {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
]
])

fasta = [
[ id: 'fasta' ],
fasta = Channel.value([
[id:"fasta"],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
])

ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

ENSEMBLVEP_VEP_DEFAULT ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] )
ENSEMBLVEP_VEP_DEFAULT ( input, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, [] )
}

workflow test_ensemblvep_vep_no_fasta {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[]
]
])

ENSEMBLVEP_VEP_DEFAULT ( input, "WBcel235", "caenorhabditis_elegans", "108", [], [[], []], [] )
ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

ENSEMBLVEP_VEP_DEFAULT ( input, vep_genome, vep_species, vep_cache_version, vep_cache, [[], []], [] )
}

workflow test_ensemblvep_vep_fasta_custom {
input = [
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
[ file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test3_vcf'], checkIfExists: true)]
]
])

fasta = [
[ id: 'fasta' ],
fasta = Channel.value([
[id:"fasta"],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
])

ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

ENSEMBLVEP_VEP_VCF_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "108", [], fasta, [] )
ENSEMBLVEP_VEP_VCF_BGZIP ( input, vep_genome, vep_species, vep_cache_version, vep_cache, fasta, [] )
}
10 changes: 2 additions & 8 deletions tests/modules/nf-core/ensemblvep/vep/nextflow.config
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Expand Up @@ -2,37 +2,31 @@ process {

publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: ENSEMBLVEP_VEP_DEFAULT {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
withName: ENSEMBLVEP_DOWNLOAD {
ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
}

withName: ENSEMBLVEP_VEP_JSON {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
ext.args = '--json'
}

withName: ENSEMBLVEP_VEP_TAB {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
ext.args = '--tab'
}

withName: ENSEMBLVEP_VEP_VCF {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
ext.args = '--vcf'
}

withName: ENSEMBLVEP_VEP_VCF_BGZIP {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
ext.args = '--vcf --compress_output bgzip'
}

withName: ENSEMBLVEP_VEP_VCF_GZIP {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
ext.args = '--vcf --compress_output gzip'
}

withName: ENSEMBLVEP_VEP_CUSTOM {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
ext.args = '--custom test2.vcf,,vcf,exact,0,TOPMED --custom test3.vcf,,vcf,exact,0,TOPMED'
}
}
22 changes: 18 additions & 4 deletions tests/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
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Expand Up @@ -2,16 +2,26 @@

nextflow.enable.dsl = 2

include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_ENSEMBLVEP_DEFAULT } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf'
include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_ENSEMBLVEP_CUSTOM } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf'
include { ENSEMBLVEP_DOWNLOAD } from '../../../../modules/nf-core/ensemblvep/download/main'
include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_ENSEMBLVEP_CUSTOM } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep/main'
include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_ENSEMBLVEP_DEFAULT } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep/main'

vep_cache_version = "110"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
vep_cache_input = Channel.of([[id:"${vep_cache_version}_${vep_genome}"], vep_genome, vep_species, vep_cache_version])

workflow vcf_annotate_ensemblvep {
input = Channel.of([
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true), []
])

VCF_ANNOTATE_ENSEMBLVEP_DEFAULT ( input, [[],[]], "WBcel235", "caenorhabditis_elegans", "108", [], [] )
ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

VCF_ANNOTATE_ENSEMBLVEP_DEFAULT ( input, [[],[]], vep_genome, vep_species, vep_cache_version, vep_cache, [] )
}

workflow vcf_annotate_ensemblvep_custom {
Expand All @@ -24,5 +34,9 @@ workflow vcf_annotate_ensemblvep_custom {
]
])

VCF_ANNOTATE_ENSEMBLVEP_CUSTOM ( input, [[],[]], "WBcel235", "caenorhabditis_elegans", "108", [], [] )
ENSEMBLVEP_DOWNLOAD(vep_cache_input)

vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }

VCF_ANNOTATE_ENSEMBLVEP_CUSTOM ( input, [[],[]], vep_genome, vep_species, vep_cache_version, vep_cache, [] )
}
12 changes: 6 additions & 6 deletions tests/subworkflows/nf-core/vcf_annotate_ensemblvep/nextflow.config
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Expand Up @@ -2,16 +2,16 @@ process {

publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: ENSEMBLVEP_VEP {
container = 'docker.io/nfcore/vep:108.2.WBcel235'
}

withName: vcf_annotate_ensemblvep_custom:VCF_ANNOTATE_ENSEMBLVEP_CUSTOM:ENSEMBLVEP_VEP {
ext.args = '--custom test2.vcf,,vcf,exact,0,TOPMED --custom test3.vcf,,vcf,exact,0,TOPMED'
withName: ENSEMBLVEP_DOWNLOAD {
ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
}

withName: TABIX_TABIX {
ext.prefix = { "${meta.id}_vep.ann" }
}

withName: vcf_annotate_ensemblvep_custom:VCF_ANNOTATE_ENSEMBLVEP_CUSTOM:ENSEMBLVEP_VEP {
ext.args = '--custom test2.vcf,,vcf,exact,0,TOPMED --custom test3.vcf,,vcf,exact,0,TOPMED'
}

}
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