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Add parameter glimpse version #308

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d5a13aa
Add parameter glimpse version
LouisLeNezet Sep 2, 2026
de8bce4
Update all tests
LouisLeNezet Sep 2, 2026
68ca6c1
Update test data
LouisLeNezet Sep 3, 2026
2c408e1
Update map
LouisLeNezet Sep 3, 2026
5869c21
Update config
LouisLeNezet Sep 3, 2026
4314540
Update map
LouisLeNezet Sep 3, 2026
535852e
Update test
LouisLeNezet Sep 3, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#248](https://github.com/nf-core/phaseimpute/pull/248) - Add chromosomes concatenation to `BAM_GL_BCFTOOLS`
- [#259](https://github.com/nf-core/phaseimpute/pull/259) - Add `publish_all` arguments to all workflow level nf-test.
- [#272](https://github.com/nf-core/phaseimpute/pull/272) - Add genetic map detection and convertion for all phasing and imputation tools. Update usage.
- [#](https://github.com/nf-core/phaseimpute/pull/) - Add `chunk_version` parameter to control which Glimpse version to use to chunk.

### `Changed`

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1 change: 1 addition & 0 deletions conf/test_full.config
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Expand Up @@ -33,6 +33,7 @@ params {
normalize = true
compute_freq = false
phase = false
chunk_version = "V2"

@atrigila atrigila Sep 4, 2026

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Can you update usage.md to document these new changes, please? Thank you :)


// Validation optional args
min_val_gl = 0
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5 changes: 3 additions & 2 deletions main.nf
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Expand Up @@ -60,7 +60,7 @@ workflow NFCORE_PHASEIMPUTE {
rename_chr // parameter: rename chromosome prefix
max_chr_names // parameter: max number of chr to show in message
params_simulate // map: parameters use for simulation step [depth: float, genotype: path]
params_panelprep // map: parameters use for panelprep step [normalize: boolean, remove_samples: string, compute_freq: boolean, phase: boolean, chunk_model: string ]
params_panelprep // map: parameters use for panelprep step [normalize: boolean, remove_samples: string, compute_freq: boolean, phase: boolean, chunk_model: string, chunk_version: string ]
params_impute // map: parameters use for imputation step [batch_size: integer, k_val: integer, n_gen: integer, buffer: integer]
params_validate // map: parameters use for validation step [bins: string, min_val_gl: float, min_val_dp: integer]
params_multiqc // map: parameters use for multiqc report [config: path, logo: path, methods_description: string]
Expand Down Expand Up @@ -166,7 +166,8 @@ workflow {
remove_samples: params.remove_samples,
compute_freq : params.compute_freq,
phase : params.phase,
chunk_model : params.chunk_model
chunk_model : params.chunk_model,

@atrigila atrigila Sep 4, 2026

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Chunk model won't apply to both v1 and v2, right? Should we have a warning if you provide a v2 model and request a v1 version?

@atrigila atrigila Sep 4, 2026

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Maybe a test case can be added to cover for this scenario as well

chunk_version : params.chunk_version
]

def params_impute = [
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -25,6 +25,7 @@ params {
compute_freq = false
remove_samples = null
chunk_model = 'sequential'
chunk_version = 'V1'

// ChrCheck parameters
rename_chr = false
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7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -144,6 +144,13 @@
"enum": ["recursive", "sequential"],
"default": "sequential",
"hidden": true
},
"chunk_version": {
"type": "string",
"description": "Glimpse version to use for chunking",
"enum": ["V1", "V2"],
"default": "V1",
"hidden": true
}
}
},
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56 changes: 17 additions & 39 deletions subworkflows/local/vcf_chunk_glimpse/main.nf
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Expand Up @@ -6,52 +6,30 @@ workflow VCF_CHUNK_GLIMPSE {
take:
ch_reference // channel (mandatory): [ [panel_id, chr], vcf, csi ]
ch_map // channel (optional) : [ [panel_id, chr], map ]
chunk_model // channel : model
chunk_model // value : model
chunk_version // value : glimpse version to use

main:

// Add chromosome to channel
ch_vcf_csi_chr = ch_reference
.map{metaPC, vcf, csi -> [metaPC, vcf, csi, metaPC.chr]}

// Make chunks with Glimpse1
GLIMPSE_CHUNK(ch_vcf_csi_chr)

// Rearrange chunks into channel for QUILT
ch_chunks_quilt = GLIMPSE_CHUNK.out.chunk_chr
.splitText()
.map { metaPC, line ->
def fields = line.split("\t")
def startEnd = fields[2].split(':')[1].split('-')
[metaPC, metaPC.chr, startEnd[0], startEnd[1]]
}

// Rearrange chunks into channel for GLIMPSE1 and GLIMPSE2
ch_chunks_glimpse1 = GLIMPSE_CHUNK.out.chunk_chr
.splitCsv(
header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'],
sep: "\t", skip: 0
)
.map { metaPC, it -> [metaPC, it["RegionIn"], it["RegionOut"]]}

ch_input_glimpse2 = ch_vcf_csi_chr
.combine(ch_map, by:0)

GLIMPSE2_CHUNK(ch_input_glimpse2, chunk_model)

// Rearrange channels
ch_chunks_glimpse2 = GLIMPSE2_CHUNK.out.chunk_chr
.splitCsv(
header: [
'ID', 'Chr', 'RegionBuf', 'RegionCnk', 'WindowCm',
'WindowMb', 'NbTotVariants', 'NbComVariants'
], sep: "\t", skip: 0
)
.map { metaPC, it -> [metaPC, it["RegionBuf"], it["RegionCnk"]]}
if (chunk_version == "V1") {
// Make chunks with Glimpse1
GLIMPSE_CHUNK(ch_vcf_csi_chr)

ch_chunks = GLIMPSE_CHUNK.out.chunk_chr
} else if (chunk_version == "V2") {
ch_input_glimpse2 = ch_vcf_csi_chr
.combine(ch_map, by:0)

GLIMPSE2_CHUNK(ch_input_glimpse2, chunk_model)
ch_chunks = GLIMPSE2_CHUNK.out.chunk_chr
} else {
error ("Parameter chunk_version should be V1 or V2, found: ${chunk_version}.")

@atrigila atrigila Sep 4, 2026

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I think this is not needed since it should fail before this if a different one is provided. It should fail and error due to the schema which only allows enums.

}

emit:
chunks = GLIMPSE_CHUNK.out.chunk_chr // channel: [ [panel_id, chr], txt ]
chunks_quilt = ch_chunks_quilt // channel: [ [panel_id, chr], chr, start, end ]
chunks_glimpse1 = ch_chunks_glimpse1 // channel: [ [panel_id, chr], chr, region1, region2 ]
chunks_glimpse2 = ch_chunks_glimpse2 // channel: [ [panel_id, chr], chr, region1, region2 ]
chunks = ch_chunks // channel: [ [panel_id, chr], txt ]
}
6 changes: 6 additions & 0 deletions subworkflows/local/vcf_chunk_glimpse/meta.yml
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Expand Up @@ -43,6 +43,12 @@ input:
- recursive
- sequential
- uniform-number-variants
- chunk_version:
description: Glimpse version to chunk
type: string
enum:
- V1
- V2
output:
- chunks:
description: Channel with chunks files
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65 changes: 57 additions & 8 deletions subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
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Expand Up @@ -17,7 +17,7 @@ nextflow_workflow {
tag "glimpse2"
tag "glimpse2/chunk"

test("Chunks with Map") {
test("Chunks with Map - V1") {
when {
workflow {
"""
Expand All @@ -36,14 +36,15 @@ nextflow_workflow {
input[1] = channel.of(
[
[panel_id: "1000GP", chr: "chr22"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr22.glimpse.map", checkIfExist:true)
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.glimpse.map", checkIfExist:true)
],
[
[panel_id: "1000GP", chr: "chr21"],
file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr21.glimpse.map", checkIfExist:true)
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExist:true)
]
)
input[2] = "recursive"
input[3] = "V1"
"""
}
}
Expand All @@ -52,7 +53,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out,
workflow.out.chunks,
workflow.out.chunks.collect{
path(it[1]).readLines()
}
Expand All @@ -62,7 +63,53 @@ nextflow_workflow {
}
}

test("Chunks without Map") {
test("Chunks with Map - V2") {
when {
workflow {
"""
input[0] = channel.of(
[
[panel_id: "1000GP", chr: "chr22"],
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),
],
[
[panel_id: "1000GP", chr: "chr21"],
file(params.pipelines_testdata_base_path + "hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz", checkIfExist:true),
file(params.pipelines_testdata_base_path + "hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz.csi", checkIfExist:true),
]
)
input[1] = channel.of(
[
[panel_id: "1000GP", chr: "chr22"],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.glimpse.map", checkIfExist:true)
],
[
[panel_id: "1000GP", chr: "chr21"],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExist:true)
]
)
input[2] = "recursive"
input[3] = "V2"
"""
}
}

then {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out.chunks,
workflow.out.chunks.collect{
path(it[1]).readLines()
}
).match()
}
)
}
}

test("Chunks without Map - V1") {
when {
workflow {
"""
Expand All @@ -83,6 +130,7 @@ nextflow_workflow {
[[panel_id: "1000GP", chr: "chr21"], []]
)
input[2] = "recursive"
input[3] = "V1"
"""
}
}
Expand All @@ -91,7 +139,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out,
workflow.out.chunks,
workflow.out.chunks.collect{
path(it[1]).readLines()
}
Expand All @@ -101,7 +149,7 @@ nextflow_workflow {
}
}

test("Chunks with sequential model") {
test("Chunks with sequential model - V2") {
when {
workflow {
"""
Expand All @@ -122,6 +170,7 @@ nextflow_workflow {
[[panel_id: "1000GP", chr: "chr21"], []]
)
input[2] = "sequential"
input[3] = "V2"
"""
}
}
Expand All @@ -130,7 +179,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out,
workflow.out.chunks,
workflow.out.chunks.collect{
path(it[1]).readLines()
}
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