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Update vcf2maf and add stub tests #7202

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Update vcf2maf and add stub tests #7202

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2c0a980
update and add stubs
famosab Dec 11, 2024
0a799e0
update snap
famosab Dec 11, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/vcf2maf/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ channels:
- bioconda
dependencies:
- bioconda::ensembl-vep=106.1
- bioconda::vcf2maf=1.6.21
- bioconda::vcf2maf=1.6.22
31 changes: 23 additions & 8 deletions modules/nf-core/vcf2maf/main.nf
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Expand Up @@ -6,8 +6,8 @@ process VCF2MAF {
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0':
'biocontainers/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7c/7cbf9421f0bee23a93a35c5d0c7166ac1e89a40008d8e474cecfddb93226bf65/data':
'community.wave.seqera.io/library/ensembl-vep_vcf2maf:2d40b60b4834af73' }"

input:
tuple val(meta), path(vcf) // Use an uncompressed VCF file!
Expand All @@ -24,13 +24,10 @@ process VCF2MAF {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def vep_cache_cmd = vep_cache ? "--vep-data $vep_cache" : ""
// If VEP is present, it will find it and add it to commands.
// If VEP is not present they will be blank
def VERSION = '1.6.21' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def vep_cache_cmd = vep_cache ? "--vep-data $vep_cache" : "" // If VEP is present, it will find it and add it to commands otherwise blank
def VERSION = '1.6.22' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
if command -v vep &> /dev/null
then
if [ "$vep_cache" ]; then
VEP_CMD="--vep-path \$(dirname \$(type -p vep))"
VEP_VERSION=\$(echo -e "\\n ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')")
else
Expand All @@ -51,4 +48,22 @@ process VCF2MAF {
vcf2maf: $VERSION\$VEP_VERSION
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.6.22' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
if [ "$vep_cache" ]; then
VEP_VERSION=\$(echo -e "\\n ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')")
else
VEP_VERSION=""
fi

touch ${prefix}.maf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcf2maf: $VERSION\$VEP_VERSION
END_VERSIONS
"""
}
111 changes: 96 additions & 15 deletions modules/nf-core/vcf2maf/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,49 @@ nextflow_process {
tag "vcf2maf"
tag "untar"

setup {
run("UNTAR") {
script "../../../../modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ id:'test_genome_vep' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vep.tar.gz", checkIfExists: true)
]
"""
}
}
run("ENSEMBLVEP_DOWNLOAD") {
script "../../../../modules/nf-core/ensemblvep/download/main.nf"
process {
"""
input[0] = [
[ id:'test_genome_vep' ],
'GRCh38',
'homo_sapiens',
'113'
]
"""
}
}
}

test("Run without VEP") {

config "./nextflow.config"

when {
params {
module_args = '--ncbi-build GRCh38 --species homo_sapiens --inhibit-vep'
module_setup_args = ""
}
process {
"""
input[0] = [
[ id:'test'], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true)
]
input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ]
input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
input[2] = []
"""
}
Expand All @@ -27,30 +60,74 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
path(process.out.maf[0][1]).readLines()[5..131],
process.out.versions
process.out.versions,
path(process.out.versions[0]).readLines()
).match() },
{ assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', ' vcf2maf: 1.6.21', ' ensemblvep: 106.1'] }
)
}
}

test("Run with VEP"){
tag "vcf2maf-withVEP"
config "./nextflow.withVEP.config"

setup {
run("UNTAR") {
script "../../../../modules/nf-core/untar/main.nf"
process {
config "./nextflow.config"

when {
params {
module_args = "--ncbi-build GRCh38 --species homo_sapiens"
module_setup_args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
}
process {
"""
input[0] = [
[ id:'test_genome_vep' ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vep.tar.gz", checkIfExists: true)
]
input[0] = [
[ id:'test'], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true)
]
input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ]
input[2] = ENSEMBLVEP_DOWNLOAD.out.cache.map { it[1] }
"""
} //UNTAR.out.untar.map { it[1] }
}

then{
assertAll(
{ assert process.success },
{ assert path(process.out.maf[0][1]).readLines().size() == 2 }, // no variants, only header lines
{ assert snapshot(process.out.versions, path(process.out.versions[0]).readLines()).match() }
)
}
}

test("Run without VEP - stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test'], // meta map
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true)
]
input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ]
input[2] = []
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).readLines()
).match()
},
)
}
}

test("Run with VEP - stub"){

options "-stub"

when {
process {
Expand All @@ -68,9 +145,13 @@ nextflow_process {
then{
assertAll(
{ assert process.success },
{ assert path(process.out.maf[0][1]).readLines().size() == 2 }, // no variants, only header lines
{ assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', ' vcf2maf: 1.6.21', ' ensemblvep: 106.1'] }
{ assert snapshot(
process.out,
path(process.out.versions[0]).readLines()
).match()
},
)
}
}

}
104 changes: 100 additions & 4 deletions modules/nf-core/vcf2maf/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,96 @@
{
"Run with VEP - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
],
"maf": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
]
},
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22",
" ensemblvep: 113.0"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T16:01:35.707312"
},
"Run with VEP": {
"content": [
[
"versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
],
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22",
" ensemblvep: 113.0"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-12-11T16:49:11.083460421"
},
"Run without VEP - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,f3398fb1c4621649331dca91212dac23"
],
"maf": [
[
{
"id": "test"
},
"test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,f3398fb1c4621649331dca91212dac23"
]
},
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:49:39.498519"
},
"Run without VEP": {
"content": [
[
Expand Down Expand Up @@ -131,13 +223,17 @@
"Unknown\t0\t.\tGRCh38\tchr22\t4608\t4608\t+\tTargeted_Region\tINS\tA\tA\t<NON_REF>\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAA\t.\t.\t\t\t\t\t\t\t\t\t\t4608"
],
[
"versions.yml:md5,a81fb1aa49b86f6c9c17e3158336d930"
"versions.yml:md5,f3398fb1c4621649331dca91212dac23"
],
[
"\"VCF2MAF\":",
" vcf2maf: 1.6.22"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-09-12T15:59:58.867897"
"timestamp": "2024-12-11T15:52:16.957598"
}
}
19 changes: 10 additions & 9 deletions modules/nf-core/vcf2maf/tests/nextflow.config
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@@ -1,11 +1,12 @@
// config for running without VEP
params.species = "homo_sapiens"
params.build = "GRCh38"

process {
container = "biocontainers/vcf2maf:1.6.21--hdfd78af_0"
conda = "bioconda::vcf2maf=1.6.21"
withName: 'VCF2MAF' {
ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep"

withName: 'VCF2MAF' {
ext.args = params.module_args
}
}

withName: 'ENSEMBLVEP_DOWNLOAD' {
ext.args = params.module_setup_args
ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" }
}

}
9 changes: 0 additions & 9 deletions modules/nf-core/vcf2maf/tests/nextflow.withVEP.config
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2 changes: 0 additions & 2 deletions modules/nf-core/vcf2maf/tests/tags.yml
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