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Remove containers with cache with snpEff too #3670

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merged 8 commits into from
Jul 25, 2023
Merged

Remove containers with cache with snpEff too #3670

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4c1d845
update tests for snpeff
maxulysse Jul 25, 2023
15efb49
remove containers in config
maxulysse Jul 25, 2023
efacd59
fix cache version in tests
maxulysse Jul 25, 2023
6611609
update meta.yml
maxulysse Jul 25, 2023
d35f354
fix meta.yml
maxulysse Jul 25, 2023
aae5499
fix meta data
maxulysse Jul 25, 2023
4c135ae
fix md5sum
maxulysse Jul 25, 2023
678470c
re-enable conda tests
maxulysse Jul 25, 2023
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6 changes: 5 additions & 1 deletion modules/nf-core/snpeff/download/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,10 @@ name: SNPEFF_DOWNLOAD
description: Genetic variant annotation and functional effect prediction toolbox
keywords:
- annotation
- effect prediction
- snpeff
- variant
- vcf
tools:
- snpeff:
description: |
Expand All @@ -21,7 +25,7 @@ input:
description: |
vcf to annotate
- db:
type: value
type: string
description: |
which db to annotate with
output:
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/snpeff/snpeff/main.nf
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Expand Up @@ -10,7 +10,7 @@ process SNPEFF_SNPEFF {
input:
tuple val(meta), path(vcf)
val db
path cache
tuple val(meta2), path(cache)

output:
tuple val(meta), path("*.ann.vcf"), emit: vcf
Expand Down
4 changes: 3 additions & 1 deletion modules/nf-core/snpeff/snpeff/meta.yml
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Expand Up @@ -2,8 +2,10 @@ name: SNPEFF_SNPEFF
description: Genetic variant annotation and functional effect prediction toolbox
keywords:
- annotation
- variant
- effect prediction
- snpeff
- variant
- vcf
tools:
- snpeff:
description: |
Expand Down
8 changes: 5 additions & 3 deletions tests/modules/nf-core/snpeff/download/main.nf
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Expand Up @@ -4,8 +4,10 @@ nextflow.enable.dsl = 2

include { SNPEFF_DOWNLOAD } from '../../../../../modules/nf-core/snpeff/download/main.nf'

workflow test_snpeff_download {
input = [ [ id:'test' ], "WBcel235", "105"]
snpeff_cache_version = "105"
snpeff_genome = "WBcel235"
snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])

SNPEFF_DOWNLOAD ( input )
workflow test_snpeff_download {
SNPEFF_DOWNLOAD(snpeff_cache_input)
}
17 changes: 13 additions & 4 deletions tests/modules/nf-core/snpeff/snpeff/main.nf
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Expand Up @@ -2,13 +2,22 @@

nextflow.enable.dsl = 2

include { SNPEFF_SNPEFF } from '../../../../../modules/nf-core/snpeff/snpeff/main.nf'
include { SNPEFF_DOWNLOAD } from '../../../../../modules/nf-core/snpeff/download/main'
include { SNPEFF_SNPEFF } from '../../../../../modules/nf-core/snpeff/snpeff/main'

snpeff_cache_version = "105"
snpeff_genome = "WBcel235"
snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])

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

SNPEFF_DOWNLOAD(snpeff_cache_input)

snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()

SNPEFF_SNPEFF ( input, "WBcel235.105", [] )
SNPEFF_SNPEFF(input, "${snpeff_genome}.${snpeff_cache_version}", snpeff_cache)
}
4 changes: 0 additions & 4 deletions tests/modules/nf-core/snpeff/snpeff/nextflow.config
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Expand Up @@ -2,8 +2,4 @@ process {

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

withName: SNPEFF_SNPEFF {
container = 'docker.io/nfcore/snpeff:5.1.WBcel235'
}

}
18 changes: 14 additions & 4 deletions tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
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Expand Up @@ -3,8 +3,12 @@
nextflow.enable.dsl = 2

include { ENSEMBLVEP_DOWNLOAD } from '../../../../modules/nf-core/ensemblvep/download/main'
include { SNPEFF_DOWNLOAD } from '../../../../modules/nf-core/snpeff/download/main'
include { VCF_ANNOTATE_ENSEMBLVEP_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main'

snpeff_cache_version = "105"
snpeff_genome = "WBcel235"
snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])
vep_cache_version = "110"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
Expand Down Expand Up @@ -61,6 +65,10 @@ workflow vcf_annotate_ensemblvep_snpeff_snpeff {
]
])

SNPEFF_DOWNLOAD(snpeff_cache_input)

snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()

VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
input,
[[],[]],
Expand All @@ -69,8 +77,8 @@ workflow vcf_annotate_ensemblvep_snpeff_snpeff {
[],
[],
[],
"WBcel235.99",
[],
"${snpeff_genome}.${snpeff_cache_version}",
snpeff_cache,
["snpeff"],
5
)
Expand All @@ -93,7 +101,9 @@ workflow vcf_annotate_ensemblvep_snpeff_both {
])

ENSEMBLVEP_DOWNLOAD(vep_cache_input)
SNPEFF_DOWNLOAD(snpeff_cache_input)

snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()
vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }.first()

VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
Expand All @@ -104,8 +114,8 @@ workflow vcf_annotate_ensemblvep_snpeff_both {
vep_cache_version,
vep_cache,
[],
"WBcel235.99",
[],
"${snpeff_genome}.${snpeff_cache_version}",
snpeff_cache,
["ensemblvep", "snpeff"],
5
)
Expand Down
4 changes: 0 additions & 4 deletions tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config
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Expand Up @@ -17,8 +17,4 @@ process {
].join(" ")}
}

withName: SNPEFF_SNPEFF {
container = 'docker.io/nfcore/snpeff:5.0.WBcel235'
}

}
17 changes: 13 additions & 4 deletions tests/subworkflows/nf-core/vcf_annotate_snpeff/main.nf
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Expand Up @@ -2,13 +2,22 @@

nextflow.enable.dsl = 2

include { VCF_ANNOTATE_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_snpeff/main.nf'
include { SNPEFF_DOWNLOAD } from '../../../../modules/nf-core/snpeff/download/main'
include { VCF_ANNOTATE_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_snpeff/main'

snpeff_cache_version = "105"
snpeff_genome = "WBcel235"
snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version])

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

SNPEFF_DOWNLOAD(snpeff_cache_input)

snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first()

VCF_ANNOTATE_SNPEFF ( input, "WBcel235.99", [] )
VCF_ANNOTATE_SNPEFF ( input, "${snpeff_genome}.${snpeff_cache_version}", snpeff_cache )
}
1 change: 0 additions & 1 deletion tests/subworkflows/nf-core/vcf_annotate_snpeff/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: SNPEFF_SNPEFF {
container = 'docker.io/nfcore/snpeff:5.0.WBcel235'
publishDir = [
path: { "output/snpeff/test/" },
pattern: "*{csv,html,genes.txt}"
Expand Down
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