diff --git a/CHANGELOG.md b/CHANGELOG.md
index b93e9ed970..c59e484096 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1677](https://github.com/nf-core/sarek/pull/1677) - Migrate pytest aligner and pipeline default tests to nf-test
- [1680](https://github.com/nf-core/sarek/pull/1680) - Template update for nf-core/tools v3.0.0
- [1681](https://github.com/nf-core/sarek/pull/1681) - Template update for nf-core/tools v3.0.1
+- [1692](https://github.com/nf-core/sarek/pull/1692) - Update ensemblvep
### Fixed
@@ -39,7 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| Dependency | Old version | New version |
| ------------- | ----------- | ----------- |
| `deepvariant` | 1.5.0 | 1.6.1 |
-| `ensemblvep` | 111.0 | 112.0 |
+| `ensemblvep` | 111.0 | 113.0 |
| `fgbio` | 2.0.2 | 2.1.2 |
| `htslib` | 1.20 | 1.21 |
| `lofreq` | | 2.1.5 |
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 2ca4531a22..afc253a919 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -37,7 +37,7 @@ params {
mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
snpeff_db = 'GRCh37.87'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
}
@@ -73,7 +73,7 @@ params {
pon_tbi = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi"
sentieon_dnascope_model = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model"
snpeff_db = 'GRCh38.105'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
@@ -83,7 +83,7 @@ params {
ngscheckmate_bed = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
snpeff_db = 'GRCh37.87'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
}
@@ -92,7 +92,7 @@ params {
fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
ngscheckmate_bed ="${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed"
snpeff_db = 'GRCh38.105'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
@@ -142,7 +142,7 @@ params {
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 = 'WBcel235.105'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
}
@@ -208,7 +208,7 @@ params {
bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 'R64-1-1.105'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'R64-1-1'
vep_species = 'saccharomyces_cerevisiae'
}
@@ -235,7 +235,7 @@ params {
bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 'GRCh38.105'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
@@ -244,7 +244,7 @@ params {
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 = 'GRCh37.87'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
}
@@ -323,7 +323,7 @@ params {
known_indels_vqsr = '--resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz'
ngscheckmate_bed = "${params.igenomes_base}/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed"
snpeff_db = 'WBcel235.105'
- vep_cache_version = '111'
+ vep_cache_version = '113'
vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
}
diff --git a/modules.json b/modules.json
index 93b7b40001..fee5e24092 100644
--- a/modules.json
+++ b/modules.json
@@ -141,12 +141,12 @@
},
"ensemblvep/download": {
"branch": "master",
- "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+ "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
"installed_by": ["modules"]
},
"ensemblvep/vep": {
"branch": "master",
- "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+ "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
"installed_by": ["modules", "vcf_annotate_ensemblvep"]
},
"fastp": {
diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
index 283a45bbdf..3d36eb17c0 100644
--- a/modules/nf-core/ensemblvep/download/environment.yml
+++ b/modules/nf-core/ensemblvep/download/environment.yml
@@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- - bioconda::ensembl-vep=112.0
+ - bioconda::ensembl-vep=113.0
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
index 555c3c6645..0664a2dfb9 100644
--- a/modules/nf-core/ensemblvep/download/main.nf
+++ b/modules/nf-core/ensemblvep/download/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_DOWNLOAD {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' :
- 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }"
+ 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' :
+ 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
input:
tuple val(meta), val(assembly), val(species), val(cache_version)
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test
index ac41cc3f32..a558599578 100644
--- a/modules/nf-core/ensemblvep/download/tests/main.nf.test
+++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
process {
"""
input[0] = Channel.of([
- [id:"112_WBcel235"],
+ [id:"113_WBcel235"],
params.vep_genome,
params.vep_species,
params.vep_cache_version
@@ -41,7 +41,7 @@ nextflow_process {
process {
"""
input[0] = Channel.of([
- [id:"112_WBcel235"],
+ [id:"113_WBcel235"],
params.vep_genome,
params.vep_species,
params.vep_cache_version
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
index 9e303c5486..706bd28f19 100644
--- a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
@@ -5,282 +5,282 @@
"0": [
[
{
- "id": "112_WBcel235"
+ "id": "113_WBcel235"
},
[
[
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[
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],
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- "8000001-9000000.gz:md5,7515ee504db75bccbdd9d282429a999b",
- "9000001-10000000.gz:md5,8647b733b4eba24aaf21b3d983461b1b"
+ "1-1000000.gz:md5,1a8739457c429931923ed77596a9ee54",
+ "10000001-11000000.gz:md5,316fa1d06fc1878b6a5995f4aee3e49d",
+ "1000001-2000000.gz:md5,3926c03a091850c909bd0ccfc7133c0b",
+ "11000001-12000000.gz:md5,29ca11d2f05051cc439a0d24a9db134c",
+ "12000001-13000000.gz:md5,a46f648554e91999652019516c933754",
+ "13000001-14000000.gz:md5,167b126d1c690a0e7e25fc5ccd09fb7c",
+ "14000001-15000000.gz:md5,645554c896133c476c3083302371bcf8",
+ "15000001-16000000.gz:md5,60fc48d9a7aff6286fc6630c46bcfebc",
+ "16000001-17000000.gz:md5,07e1750d1c95a61e96774d2cf3da4d89",
+ "17000001-18000000.gz:md5,59d084309f6a975ec1066a828b5845ba",
+ "18000001-19000000.gz:md5,868c12d305dbd4d04399ec7848804328",
+ "19000001-20000000.gz:md5,6de03a00061f6a88dcbbb8ed5fc0b8dc",
+ "20000001-21000000.gz:md5,732b956f13da9ef01f9de3355d12e28b",
+ "2000001-3000000.gz:md5,7c7528266c523cad419ea25e75d9566e",
+ "3000001-4000000.gz:md5,bb2283c0cfb0e4601fc535a4d51e6f2d",
+ "4000001-5000000.gz:md5,64c7f28f554414a88c886b0bcadb3c39",
+ "5000001-6000000.gz:md5,58e7106fe577a8b5e5c698445b4f0c33",
+ "6000001-7000000.gz:md5,2e309d12cf1c1c6276585f457ceeacc2",
+ "7000001-8000000.gz:md5,08cb0600f7806608f0103187a6c9c64e",
+ "8000001-9000000.gz:md5,869333c2615f714860d17d794640d4ad",
+ "9000001-10000000.gz:md5,b85cc861c6a3b30cf6f06c8af136b383"
],
[
- "1-1000000.gz:md5,a252da6c7c69644ff29276d15796f457",
- "10000001-11000000.gz:md5,e7376cbf07ee7fd1fb8214c9bc739e64",
- "1000001-2000000.gz:md5,566d7342a45728a784af7ba5c2e630cb",
- "11000001-12000000.gz:md5,bf44ab823c1d51cb7841958761a7cd4d",
- "12000001-13000000.gz:md5,ec1494ff61067a130c05afabee046164",
- "13000001-14000000.gz:md5,2b24e155be6ae36a62e7ea3b1a0a3118",
- "14000001-15000000.gz:md5,3215b3d56cd19a305c8d8f2d1f517825",
- "15000001-16000000.gz:md5,6fa2abd0ff33750387780798dc6bd821",
- "16000001-17000000.gz:md5,c2a1e5012a895ab95662d83d387f641a",
- "17000001-18000000.gz:md5,eb398d2f8bc90b519a82588b8dcbad60",
- "2000001-3000000.gz:md5,b78320f16b4caafe9708f95b69668265",
- "3000001-4000000.gz:md5,e04cd4871f53108aaa780dbb3718b7f7",
- "4000001-5000000.gz:md5,47bd8029ef9fffb5ee2ebb0fa8b91110",
- "5000001-6000000.gz:md5,a6c404381dab5da8453b265fb0f374c3",
- "6000001-7000000.gz:md5,417b7a492977b76f823634128e3ea2da",
- "7000001-8000000.gz:md5,d0f9d030f7f4ad834d1538c7aaace5cf",
- "8000001-9000000.gz:md5,58b2eca4ddeea8d2746242b18be1dba4",
- "9000001-10000000.gz:md5,62cf6898fa164616c36117472ec10ce9"
+ "1-1000000.gz:md5,c8d97b084c159c3cb5be1fff4637dfce",
+ "10000001-11000000.gz:md5,f441f2af06fd4973749dfbfbef40fe1b",
+ "1000001-2000000.gz:md5,c42a1526a836cfacefb67e9217f648aa",
+ "11000001-12000000.gz:md5,264421c249c696b45c92e2611285fee7",
+ "12000001-13000000.gz:md5,e673d1fdbe7dc0d09bea3d11a5797d6a",
+ "13000001-14000000.gz:md5,88f4f84e63b362f1b4f800c48b37e82c",
+ "14000001-15000000.gz:md5,26282f2b305ed82fb9f8875e97361105",
+ "15000001-16000000.gz:md5,30b9132c2610d42919ba231d1adbef2a",
+ "16000001-17000000.gz:md5,3d0e975ccd1ae4e92bf1d9d915ed293f",
+ "17000001-18000000.gz:md5,7db5b3819da3df1e47fe757dc9c6f2ba",
+ "2000001-3000000.gz:md5,55f6130a8d5872bdc9f8eed231ad0f65",
+ "3000001-4000000.gz:md5,402b826dbf6993c207ad15483a44182b",
+ "4000001-5000000.gz:md5,43cf926d43db25af5724fb5077edfee1",
+ "5000001-6000000.gz:md5,f40276dbea3f6f9a75f9301d1253eb09",
+ "6000001-7000000.gz:md5,df0d2d38060d4e7c606072ae814b1f38",
+ "7000001-8000000.gz:md5,c4117cc51255c0a91c51ff43403f00f7",
+ "8000001-9000000.gz:md5,59a4ebadca27041634c58652c544c8dd",
+ "9000001-10000000.gz:md5,c54510616273a4d1bfa9d525dbbbca40"
],
- "chr_synonyms.txt:md5,c7df2db509525b8ff0d95ef927882764",
- "info.txt:md5,33ccb74a030a9a345051628c337cb8af"
+ "chr_synonyms.txt:md5,d390f0bcc6fec9786bc66b75f2d4390b",
+ "info.txt:md5,249c88c7a71464e048cca0c4b2a21198"
]
]
]
]
],
"versions": [
- "versions.yml:md5,e32852e9cba2a298b7518ce610011b14"
+ "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9"
]
}
],
"meta": {
- "nf-test": "0.8.4",
+ "nf-test": "0.9.0",
"nextflow": "24.04.4"
},
- "timestamp": "2024-09-02T13:19:08.690863"
+ "timestamp": "2024-10-21T09:09:48.574969389"
},
"celegans - download - stub": {
"content": [
@@ -288,7 +288,7 @@
"0": [
[
{
- "id": "112_WBcel235"
+ "id": "113_WBcel235"
},
[
@@ -296,12 +296,12 @@
]
],
"1": [
- "versions.yml:md5,e32852e9cba2a298b7518ce610011b14"
+ "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9"
],
"cache": [
[
{
- "id": "112_WBcel235"
+ "id": "113_WBcel235"
},
[
@@ -309,14 +309,14 @@
]
],
"versions": [
- "versions.yml:md5,e32852e9cba2a298b7518ce610011b14"
+ "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9"
]
}
],
"meta": {
- "nf-test": "0.8.4",
+ "nf-test": "0.9.0",
"nextflow": "24.04.4"
},
- "timestamp": "2024-09-02T13:19:23.308683"
+ "timestamp": "2024-10-21T09:10:03.728940123"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/download/tests/nextflow.config b/modules/nf-core/ensemblvep/download/tests/nextflow.config
index 9aa481645e..0a4ae1a6a8 100644
--- a/modules/nf-core/ensemblvep/download/tests/nextflow.config
+++ b/modules/nf-core/ensemblvep/download/tests/nextflow.config
@@ -1,5 +1,5 @@
params {
- vep_cache_version = "112"
+ vep_cache_version = "113"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
}
diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml
index 283a45bbdf..3d36eb17c0 100644
--- a/modules/nf-core/ensemblvep/vep/environment.yml
+++ b/modules/nf-core/ensemblvep/vep/environment.yml
@@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- - bioconda::ensembl-vep=112.0
+ - bioconda::ensembl-vep=113.0
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
index 5f33265b0d..7d2c82ff0a 100644
--- a/modules/nf-core/ensemblvep/vep/main.nf
+++ b/modules/nf-core/ensemblvep/vep/main.nf
@@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' :
- 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }"
+ 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' :
+ 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
input:
tuple val(meta), path(vcf), path(custom_extra_files)
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
index e68fff3c0e..3e8c0b5379 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
process {
"""
input[0] = Channel.of([
- [id:"112_WBcel235"],
+ [id:"113_WBcel235"],
params.vep_genome,
params.vep_species,
params.vep_cache_version
@@ -72,7 +72,7 @@ nextflow_process {
process {
"""
input[0] = Channel.of([
- [id:"112_WBcel235"],
+ [id:"113_WBcel235"],
params.vep_genome,
params.vep_species,
params.vep_cache_version
@@ -107,7 +107,7 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match() },
- { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v112.0") }
+ { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") }
)
}
}
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
index 1c4c0e4e9f..1df94276a4 100644
--- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
+++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
@@ -2,25 +2,25 @@
"test_ensemblvep_vep_fasta_tab_gz": {
"content": [
[
- "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559"
+ "versions.yml:md5,4fbfeb73f0d4b4aa039f17be8ba9e1f2"
]
],
"meta": {
- "nf-test": "0.8.4",
+ "nf-test": "0.9.0",
"nextflow": "24.04.4"
},
- "timestamp": "2024-09-02T10:15:18.228927"
+ "timestamp": "2024-10-21T09:12:23.474703494"
},
"test_ensemblvep_vep_fasta_vcf": {
"content": [
[
- "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559"
+ "versions.yml:md5,4fbfeb73f0d4b4aa039f17be8ba9e1f2"
]
],
"meta": {
- "nf-test": "0.8.4",
+ "nf-test": "0.9.0",
"nextflow": "24.04.4"
},
- "timestamp": "2024-09-02T10:14:50.193861"
+ "timestamp": "2024-10-21T09:11:54.343590485"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
index 9aa481645e..0a4ae1a6a8 100644
--- a/modules/nf-core/ensemblvep/vep/tests/nextflow.config
+++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config
@@ -1,5 +1,5 @@
params {
- vep_cache_version = "112"
+ vep_cache_version = "113"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
}
diff --git a/tests/.nftignore b/tests/.nftignore
index 1c607be519..b051a8987f 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,3 +1,4 @@
+annotation/**/*.vcf.{gz,gz.tbi}
csv/*.csv
multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt
multiqc/multiqc_data/gatk_base_recalibrator.txt
@@ -14,6 +15,7 @@ pipeline_info/*.{html,json,txt,yml}
preprocessing/**/*.{md,recal,sorted}.{bam,bam.bai,cram,cram.crai,table}
reference/dragmap/hash_table.{cfg,cfg.bin}
reference/dragmap/hash_table_stats.txt
+reports/EnsemblVEP/*/*.ann.summary.html
reports/fastqc/**/*_fastqc.{html,zip}
reports/markduplicates/**/*.md.cram.metrics
variant_calling/**/*.vcf.{gz,gz.tbi}
diff --git a/tests/annotation-vep.nf.test b/tests/annotation-vep.nf.test
new file mode 100644
index 0000000000..d308368fbf
--- /dev/null
+++ b/tests/annotation-vep.nf.test
@@ -0,0 +1,75 @@
+nextflow_pipeline {
+
+ name "Test pipeline"
+ script "../main.nf"
+ tag "pipeline"
+ tag "pipeline_sarek"
+
+ test("Run with profile test | --tools vep --download_cache") {
+
+ when {
+ params {
+ modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+ outdir = "$outputDir"
+ input = "${projectDir}/tests/csv/3.0/vcf_single.csv"
+ step = 'annotate'
+ download_cache = true
+ tools = 'vep'
+ }
+ }
+
+ then {
+ // stable_name: All files + folders in ${params.outdir}/ with a stable name
+ def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+ // stable_path: All files in ${params.outdir}/ with stable content
+ def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+ assertAll(
+ { assert workflow.success},
+ { assert snapshot(
+ // Number of successful tasks
+ workflow.trace.succeeded().size(),
+ // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+ // All stable path name, with a relative path
+ stable_name,
+ // All files with stable contents
+ stable_path
+ ).match() }
+ )
+ }
+ }
+
+ test("Run with profile test | --tools vep --vep_include_fasta") {
+
+ when {
+ params {
+ modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+ outdir = "$outputDir"
+ input = "${projectDir}/tests/csv/3.0/vcf_single.csv"
+ step = 'annotate'
+ vep_cache = 's3://annotation-cache/vep_cache/'
+ tools = 'vep'
+ }
+ }
+
+ then {
+ // stable_name: All files + folders in ${params.outdir}/ with a stable name
+ def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+ // stable_path: All files in ${params.outdir}/ with stable content
+ def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+ assertAll(
+ { assert workflow.success},
+ { assert snapshot(
+ // Number of successful tasks
+ workflow.trace.succeeded().size(),
+ // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+ removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+ // All stable path name, with a relative path
+ stable_name,
+ // All files with stable contents
+ stable_path
+ ).match() }
+ )
+ }
+ }
+}
diff --git a/tests/annotation-vep.nf.test.snap b/tests/annotation-vep.nf.test.snap
new file mode 100644
index 0000000000..300780733f
--- /dev/null
+++ b/tests/annotation-vep.nf.test.snap
@@ -0,0 +1,339 @@
+{
+ "Run with profile test | --tools vep --vep_include_fasta": {
+ "content": [
+ 3,
+ {
+ "ENSEMBLVEP_VEP": {
+ "ensemblvep": 113.0
+ },
+ "TABIX_TABIX": {
+ "tabix": 1.2
+ },
+ "Workflow": {
+ "nf-core/sarek": "v3.5.0dev"
+ }
+ },
+ [
+ "annotation",
+ "annotation/test",
+ "annotation/test/test_VEP.ann.vcf.gz",
+ "annotation/test/test_VEP.ann.vcf.gz.tbi",
+ "csv",
+ "multiqc",
+ "multiqc/multiqc_data",
+ "multiqc/multiqc_data/multiqc.log",
+ "multiqc/multiqc_data/multiqc_citations.txt",
+ "multiqc/multiqc_data/multiqc_data.json",
+ "multiqc/multiqc_data/multiqc_software_versions.txt",
+ "multiqc/multiqc_data/multiqc_sources.txt",
+ "multiqc/multiqc_data/vep-general-stats.txt",
+ "multiqc/multiqc_data/vep.txt",
+ "multiqc/multiqc_plots",
+ "multiqc/multiqc_plots/pdf",
+ "multiqc/multiqc_plots/pdf/vep-general-stats.pdf",
+ "multiqc/multiqc_plots/png",
+ "multiqc/multiqc_plots/png/vep-general-stats.png",
+ "multiqc/multiqc_plots/svg",
+ "multiqc/multiqc_plots/svg/vep-general-stats.svg",
+ "multiqc/multiqc_report.html",
+ "pipeline_info",
+ "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+ "reports",
+ "reports/EnsemblVEP",
+ "reports/EnsemblVEP/test",
+ "reports/EnsemblVEP/test/test_VEP.ann.summary.html"
+ ],
+ [
+ "multiqc_citations.txt:md5,afe6b13a9c0770828d9bc9515d6db802",
+ "vep-general-stats.txt:md5,2fca07ac5623e758cac3ce49d9f6e3b0",
+ "vep.txt:md5,60a5d57c60308aba2aa6206f903d27e9"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-10-24T11:49:16.737881"
+ },
+ "Run with profile test | --tools vep --download_cache": {
+ "content": [
+ 4,
+ {
+ "ENSEMBLVEP_VEP": {
+ "ensemblvep": 113.0
+ },
+ "TABIX_TABIX": {
+ "tabix": 1.2
+ },
+ "Workflow": {
+ "nf-core/sarek": "v3.5.0dev"
+ }
+ },
+ [
+ "annotation",
+ "annotation/test",
+ "annotation/test/test_VEP.ann.vcf.gz",
+ "annotation/test/test_VEP.ann.vcf.gz.tbi",
+ "cache",
+ "cache/vep_cache",
+ "cache/vep_cache/caenorhabditis_elegans",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/1-1000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/10000001-11000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/1000001-2000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/11000001-12000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/12000001-13000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/13000001-14000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/14000001-15000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/15000001-16000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/2000001-3000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/3000001-4000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/4000001-5000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/5000001-6000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/6000001-7000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/7000001-8000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/8000001-9000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/I/9000001-10000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/II",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/II/1-1000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/II/10000001-11000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/II/1000001-2000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/II/11000001-12000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/II/12000001-13000000.gz",
+ "cache/vep_cache/caenorhabditis_elegans/113_WBcel235/II/13000001-14000000.gz",
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+ },
+ "timestamp": "2024-10-23T15:00:39.082074"
+ }
+}
\ No newline at end of file
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index 2cc8390044..d856905805 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -495,15 +495,6 @@ snpeff:
- tests/csv/3.0/vcf_single.csv
- tests/test_annotation_snpeff.yml
-## vep
-vep:
- - conf/modules/annotate.config
- - modules/nf-core/ensemblvep/vep/**
- - modules/nf-core/tabix/bgziptabix/**
- - subworkflows/nf-core/vcf_annotate_ensemblvep/**
- - tests/csv/3.0/vcf_single.csv
- - tests/test_annotation_vep.yml
-
## bcfann
bcfann:
- conf/modules/annotate.config
diff --git a/tests/test_annotation_vep.yml b/tests/test_annotation_vep.yml
deleted file mode 100644
index 0965631832..0000000000
--- a/tests/test_annotation_vep.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-- name: Run VEP
- command: nextflow run main.nf -profile test,annotation --tools vep --outdir results --download_cache
- tags:
- - annotation
- - vep
- files:
- - path: results/annotation/test/test_VEP.ann.vcf.gz
- # binary changes md5sums on reruns
- - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
- # binary changes md5sums on reruns
- - path: results/multiqc
- - path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html
- contains: ["test.vcf.gz</pre></td></tr><tr><td>Output file</td><td><pre>test_VEP.ann.vcf.gz"]
-- name: Run VEP with fasta
- command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --outdir results --download_cache
- tags:
- - annotation
- - vep
- files:
- - path: results/annotation/test/test_VEP.ann.vcf.gz
- # binary changes md5sums on reruns
- - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi
- # binary changes md5sums on reruns
- - path: results/multiqc
- - path: results/reports/EnsemblVEP/test/test_VEP.ann.summary.html
- # text-based file changes md5sums on reruns
- contains: ["test.vcf.gz</pre></td></tr><tr><td>Output file</td><td><pre>test_VEP.ann.vcf.gz"]