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Add genetic map support for MINIMAC4 sbwf #222

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#188](https://github.com/nf-core/phaseimpute/pull/188) - Add documentation for all subworkflows.
- [#210](https://github.com/nf-core/phaseimpute/pull/200) - Add BEAGLE5 support for genotype imputation.
- [#211](https://github.com/nf-core/phaseimpute/pull/211) - Add MINIMAC4 support for genotype imputation.
- [#222](https://github.com/nf-core/phaseimpute/pull/222) - Add genetic map support for `MINIMAC4`.

### `Changed`

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2 changes: 1 addition & 1 deletion subworkflows/local/vcf_impute_minimac4/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ input:
Need to have "chr" as chromosome name
- map:
type: file
description: PLINK format genetic map files
description: Minimac format genetic map files
pattern: "*.map"
output:
- vcf_tbi:
Expand Down
75 changes: 41 additions & 34 deletions subworkflows/local/vcf_impute_minimac4/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ nextflow_workflow {
tag "minimac4/compressref"
tag "minimac4/impute"

test("Impute with minimac4 one vcf") {
test("Impute with minimac4 one vcf no map") {

when {
workflow {
Expand All @@ -41,14 +41,15 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out.versions,
workflow.out.vcf_index.collect{[
workflow.out.vcf_tbi.collect{[
it[0],
file(it[1]).name,
file(it[2]).name
] },
workflow.out.vcf_index.collect{ path(it[1]).vcf.summary },
workflow.out.vcf_index.collect{ path(it[1]).vcf.variantsMD5 }
path(it[1]).getFileName().toString(),
path(it[2]).getFileName().toString(),
path(it[1]).vcf.summary,
path(it[1]).vcf.header.getGenotypeSamples().sort(),
path(it[1]).vcf.variantsMD5
]},
workflow.out.versions.collect{ path(it).yaml }
).match() }
)
}
Expand All @@ -71,7 +72,7 @@ nextflow_workflow {
])
input[2] = Channel.of([
[chr: "chr22"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr22.glimpse.map", checkIfExist:true)
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr22.minimac.map", checkIfExist:true)
])
input[3] = Channel.of([[chr: "chr22"], [], [], [], []])
"""
Expand All @@ -82,20 +83,21 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out.versions,
workflow.out.vcf_index.collect{[
workflow.out.vcf_tbi.collect{[
it[0],
file(it[1]).name,
file(it[2]).name
] },
workflow.out.vcf_index.collect{ path(it[1]).vcf.summary },
workflow.out.vcf_index.collect{ path(it[1]).vcf.variantsMD5 }
path(it[1]).getFileName().toString(),
path(it[2]).getFileName().toString(),
path(it[1]).vcf.summary,
path(it[1]).vcf.header.getGenotypeSamples().sort(),
path(it[1]).vcf.variantsMD5
]},
workflow.out.versions.collect{ path(it).yaml }
).match() }
)
}
}

test("Impute with minimac4 two vcf") {
test("Impute with minimac4 two vcf with map") {

when {
workflow {
Expand All @@ -117,7 +119,10 @@ nextflow_workflow {
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.s.norel.vcf.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.s.norel.vcf.gz.csi", checkIfExist:true)
])
input[2] = Channel.of([[chr: "chr22"], []])
input[2] = Channel.of([
[chr: "chr22"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr22.minimac.map", checkIfExist:true)
])
input[3] = Channel.of([[chr: "chr22"], [], [], [], []])
"""
}
Expand All @@ -127,20 +132,21 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out.versions,
workflow.out.vcf_index.collect{[
workflow.out.vcf_tbi.collect{[
it[0],
file(it[1]).name,
file(it[2]).name
] },
workflow.out.vcf_index.collect{ path(it[1]).vcf.summary },
workflow.out.vcf_index.collect{ path(it[1]).vcf.variantsMD5 }
path(it[1]).getFileName().toString(),
path(it[2]).getFileName().toString(),
path(it[1]).vcf.summary,
path(it[1]).vcf.header.getGenotypeSamples().sort(),
path(it[1]).vcf.variantsMD5
]},
workflow.out.versions.collect{ path(it).yaml }
).match() }
)
}
}

test("Impute with minimac4 one vcf with sites") {
test("Impute with minimac4 one vcf with sites, no map") {

when {
workflow {
Expand All @@ -157,7 +163,7 @@ nextflow_workflow {
])
input[2] = Channel.of([
[chr: "chr22"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr22.glimpse.map", checkIfExist:true)
[]
])
input[3] = Channel.of([
[chr: "chr22"],
Expand All @@ -174,14 +180,15 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out.versions,
workflow.out.vcf_index.collect{[
workflow.out.vcf_tbi.collect{[
it[0],
file(it[1]).name,
file(it[2]).name
] },
workflow.out.vcf_index.collect{ path(it[1]).vcf.summary },
workflow.out.vcf_index.collect{ path(it[1]).vcf.variantsMD5 }
path(it[1]).getFileName().toString(),
path(it[2]).getFileName().toString(),
path(it[1]).vcf.summary,
path(it[1]).vcf.header.getGenotypeSamples().sort(),
path(it[1]).vcf.variantsMD5
]},
workflow.out.versions.collect{ path(it).yaml }
).match() }
)
}
Expand Down
174 changes: 75 additions & 99 deletions subworkflows/local/vcf_impute_minimac4/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,142 +1,118 @@
{
"Impute with minimac4 two vcf": {
"Impute with minimac4 one vcf no map": {
"content": [
[
"versions.yml:md5,373fe12da367d3891473f487a9536d04",
"versions.yml:md5,99b8cb34e87147cec893f4bcf7a9b244",
"versions.yml:md5,a4842af8fedc3522b989d4ee28f08d80"

],
[
[
{
"id": "NA12878",
"panel": "1000GP",
"chr": "chr22",
"tools": "minimac4"
},
"NA12878.vcf.gz",
"NA12878.vcf.gz.csi"
],
[
{
"id": "NA19401",
"panel": "1000GP",
"chr": "chr22",
"tools": "minimac4"
},
"NA19401.vcf.gz",
"NA19401.vcf.gz.csi"
]
],
[
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=903, phased=true, phasedAutodetect=true]",
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=903, phased=true, phasedAutodetect=true]"
],
[
"c4327d84f0355b88979ec03dd037514b",
"1b1c49668e75466692e0f586fc47f747"
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_COMPRESSREF": {
"minimac4": "4.1.6"
}
},
{
"VCF_IMPUTE_MINIMAC4:BCFTOOLS_INDEX": {
"bcftools": 1.21
}
},
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_IMPUTE": {
"minimac4": "4.1.6"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-11T12:36:15.295537018"
"timestamp": "2025-11-18T14:57:42.013572476"
},
"Impute with minimac4 one vcf": {
"Impute with minimac4 two vcf with map": {
"content": [
[
"versions.yml:md5,373fe12da367d3891473f487a9536d04",
"versions.yml:md5,99b8cb34e87147cec893f4bcf7a9b244",
"versions.yml:md5,a4842af8fedc3522b989d4ee28f08d80"
],
[
[
{
"id": "NA12878",
"panel": "1000GP",
"chr": "chr22",
"tools": "minimac4"
},
"NA12878.vcf.gz",
"NA12878.vcf.gz.csi"
]
],
[
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=903, phased=true, phasedAutodetect=true]"

],
[
"c4327d84f0355b88979ec03dd037514b"
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_COMPRESSREF": {
"minimac4": "4.1.6"
}
},
{
"VCF_IMPUTE_MINIMAC4:BCFTOOLS_INDEX": {
"bcftools": 1.21
}
},
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_IMPUTE": {
"minimac4": "4.1.6"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-11T12:35:46.826956402"
"timestamp": "2025-11-18T14:58:06.940677488"
},
"Impute with minimac4 one vcf with sites": {
"Impute with minimac4 one vcf with sites, no map": {
"content": [
[
"versions.yml:md5,373fe12da367d3891473f487a9536d04",
"versions.yml:md5,99b8cb34e87147cec893f4bcf7a9b244",
"versions.yml:md5,a4842af8fedc3522b989d4ee28f08d80"

],
[
[
{
"id": "NA12878",
"panel": "1000GP",
"chr": "chr22",
"tools": "minimac4"
},
"NA12878.vcf.gz",
"NA12878.vcf.gz.csi"
]
],
[
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=903, phased=true, phasedAutodetect=true]"
],
[
"ab57a5554b8c01ae0494318233d1b1dd"
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_COMPRESSREF": {
"minimac4": "4.1.6"
}
},
{
"VCF_IMPUTE_MINIMAC4:BCFTOOLS_INDEX": {
"bcftools": 1.21
}
},
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_IMPUTE": {
"minimac4": "4.1.6"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-11T12:36:28.874465664"
"timestamp": "2025-11-18T14:58:19.03416638"
},
"Impute with minimac4 one vcf with map": {
"content": [
[
"versions.yml:md5,373fe12da367d3891473f487a9536d04",
"versions.yml:md5,99b8cb34e87147cec893f4bcf7a9b244",
"versions.yml:md5,a4842af8fedc3522b989d4ee28f08d80"
],
[
[
{
"id": "NA12878",
"panel": "1000GP",
"chr": "chr22",
"tools": "minimac4"
},
"NA12878.vcf.gz",
"NA12878.vcf.gz.csi"
]
],
[
"VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=903, phased=true, phasedAutodetect=true]"

],
[
"ab57a5554b8c01ae0494318233d1b1dd"
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_COMPRESSREF": {
"minimac4": "4.1.6"
}
},
{
"VCF_IMPUTE_MINIMAC4:BCFTOOLS_INDEX": {
"bcftools": 1.21
}
},
{
"VCF_IMPUTE_MINIMAC4:MINIMAC4_IMPUTE": {
"minimac4": "4.1.6"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-11T12:36:00.295884864"
"timestamp": "2025-11-18T15:00:50.226056725"
}
}