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Merged
LouisLeNezet merged 16 commits into from
Dec 4, 2025
Merged

Update test files for Glimpse #9467

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79851ec
Update glimpse
Nov 26, 2025
c094984
Update chunk
Nov 26, 2025
e8ce50b
Update concordance
Nov 26, 2025
129d099
Revert changes
Nov 26, 2025
5a61f40
Fix glimpse test
Nov 26, 2025
b0993c0
Fix glimpse
Nov 26, 2025
256d129
Fix glimpse2 tests
Nov 26, 2025
8e18dc9
Update sbwf
Nov 26, 2025
159b394
Merge branch 'master' into upd_glimpse
LouisLeNezet Nov 26, 2025
62b7c1e
Remove old snapshots
Nov 26, 2025
fbcd995
Merge branch 'master' into upd_glimpse
LouisLeNezet Nov 27, 2025
7507e0a
Update glimpse
LouisLeNezet Nov 27, 2025
c6c487e
Update modules/nf-core/glimpse2/concordance/tests/main.nf.test
LouisLeNezet Nov 27, 2025
eb23dce
Merge branch 'master' into upd_glimpse
LouisLeNezet Nov 27, 2025
a245ad4
Update test
LouisLeNezet Nov 27, 2025
72c3408
Merge branch 'master' into upd_glimpse
LouisLeNezet Dec 4, 2025
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1 change: 1 addition & 0 deletions modules/nf-core/glimpse/chunk/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ process GLIMPSE_CHUNK {

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.txt

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15 changes: 9 additions & 6 deletions modules/nf-core/glimpse/chunk/tests/main.nf.test
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Expand Up @@ -3,22 +3,25 @@ nextflow_process {
name "Test Process GLIMPSE_CHUNK"
script "../main.nf"
process "GLIMPSE_CHUNK"
config "./nextflow.config"

tag "glimpse"
tag "glimpse/chunk"
tag "modules_nfcore"
tag "modules"

test("Should run without failures") {
config "modules/nf-core/glimpse/chunk/tests/nextflow.config"

test("homo_sapiens - vcf chr 22") {
when {
params{
glimpse_args = "--window-size 2000000 --buffer-size 200000"
}
process {
"""
input[0] = [
[ id:'input' ], // meta map
file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true),
"chr21"
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true),
"chr22"
]
"""
}
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12 changes: 8 additions & 4 deletions modules/nf-core/glimpse/chunk/tests/main.nf.test.snap
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@@ -1,13 +1,13 @@
{
"Should run without failures": {
"homo_sapiens - vcf chr 22": {
"content": [
{
"0": [
[
{
"id": "input"
},
"input.txt:md5,9e5562b3f94857b8189b59849ce65cfb"
"input.txt:md5,38bc015bc7bb9f4fc0fdb08a698cfc78"
]
],
"1": [
Expand All @@ -18,14 +18,18 @@
{
"id": "input"
},
"input.txt:md5,9e5562b3f94857b8189b59849ce65cfb"
"input.txt:md5,38bc015bc7bb9f4fc0fdb08a698cfc78"
]
],
"versions": [
"versions.yml:md5,a523ef8d6391ddeff47bfd30b606d628"
]
}
],
"timestamp": "2023-10-16T15:55:52.457257547"
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-26T19:06:32.115560314"
}
}
5 changes: 1 addition & 4 deletions modules/nf-core/glimpse/chunk/tests/nextflow.config
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@@ -1,9 +1,6 @@
process {
withName: GLIMPSE_CHUNK {
ext.args = [
"--window-size 2000000",
"--buffer-size 200000"
].join(' ')
ext.args = { "${params.glimpse_args}" }
ext.prefix = { "${meta.id}" }
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/glimpse/concordance/main.nf
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Expand Up @@ -20,7 +20,6 @@ process GLIMPSE_CONCORDANCE {
tuple val(meta), path("*.rsquare.grp.txt.gz"), emit: rsquare_grp
tuple val(meta), path("*.rsquare.spl.txt.gz"), emit: rsquare_spl
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

Expand All @@ -42,13 +41,14 @@ process GLIMPSE_CONCORDANCE {
$bins_cmd

cat <<-END_VERSIONS > versions.yml
"${task.process}":
glimpse: "\$(GLIMPSE_concordance --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
"${task.process}":
glimpse: "\$(GLIMPSE_concordance --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
echo "" | gzip > ${prefix}.error.cal.txt.gz
echo "" | gzip > ${prefix}.error.grp.txt.gz
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76 changes: 15 additions & 61 deletions modules/nf-core/glimpse/concordance/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@ nextflow_process {
script "../main.nf"
process "GLIMPSE_CONCORDANCE"

config "./nextflow.config"

tag "modules"
tag "modules_nfcore"
tag "glimpse"
Expand All @@ -12,64 +14,21 @@ nextflow_process {
tag "bcftools/index"

test("test_glimpse_concordance") {
setup {
run("GLIMPSE_PHASE") {
script "../../phase/main.nf"
process {
"""
ch_sample = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
region = Channel.fromList([
["chr21:16600000-16750000","chr21:16650000-16700000"]
])
input_vcf = Channel.of([
[ id:'input'], // meta map
file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
])
ref_panel = Channel.of([
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
])
ch_map = Channel.of([
file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
])

input[0] = input_vcf
| combine(ch_sample)
| combine(region)
| combine(ref_panel)
| combine(ch_map)
"""
}
}
run("BCFTOOLS_INDEX") {
script "../../../bcftools/index/main.nf"
process {
"""
input[0] = GLIMPSE_PHASE.out.phased_variants
"""
}
}
}
when {
process {
"""
allele_freq = Channel.fromList([
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
]).collect()
truth = Channel.fromList([
file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
]).collect()
estimate = GLIMPSE_PHASE.out.phased_variants
| join (BCFTOOLS_INDEX.out.csi)
input[0] = estimate
| combine (allele_freq)
| combine (truth)
| combine (["chr21"])
input[1] = []
input[2] = []
input[0] = channel.of([
[ id: "NA12878" ],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz",checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi",checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.sites.vcf.gz",checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.sites.vcf.gz.csi",checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz",checkIfExists:true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi",checkIfExists:true),
"chr21"
])
input[1] = 0.7
input[2] = 3
input[3] = []
"""
}
Expand All @@ -78,12 +37,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.errors_cal,
process.out.errors_spl,
process.out.rsquare_spl,
process.out.versions
).match() }
{ assert snapshot(process.out).match() }
)
}

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119 changes: 90 additions & 29 deletions modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,38 +1,99 @@
{
"test_glimpse_concordance": {
"content": [
[
[
{
"id": "input"
},
"input.error.cal.txt.gz:md5,15c6a120d9fd3ac8c0ff6a6aedc76571"
{
"0": [
[
{
"id": "NA12878"
},
"NA12878.error.cal.txt.gz:md5,b4af39e7acfebd69f2fe5fa496551a32"
]
],
"1": [
[
{
"id": "NA12878"
},
"NA12878.error.grp.txt.gz:md5,069e311f252ff6b6e748a68ce0bcb499"
]
],
"2": [
[
{
"id": "NA12878"
},
"NA12878.error.spl.txt.gz:md5,284843acf1662f2aeafc6fe5c47e629f"
]
],
"3": [
[
{
"id": "NA12878"
},
"NA12878.rsquare.grp.txt.gz:md5,06c70a1e2047710d6752b9d98e45cea0"
]
],
"4": [
[
{
"id": "NA12878"
},
"NA12878.rsquare.spl.txt.gz:md5,30a00f0b1de47fd63414d819b4304ded"
]
],
"5": [
"versions.yml:md5,b6c06f9736c60f9f548c3c082b522025"
],
"errors_cal": [
[
{
"id": "NA12878"
},
"NA12878.error.cal.txt.gz:md5,b4af39e7acfebd69f2fe5fa496551a32"
]
],
"errors_grp": [
[
{
"id": "NA12878"
},
"NA12878.error.grp.txt.gz:md5,069e311f252ff6b6e748a68ce0bcb499"
]
],
"errors_spl": [
[
{
"id": "NA12878"
},
"NA12878.error.spl.txt.gz:md5,284843acf1662f2aeafc6fe5c47e629f"
]
],
"rsquare_grp": [
[
{
"id": "NA12878"
},
"NA12878.rsquare.grp.txt.gz:md5,06c70a1e2047710d6752b9d98e45cea0"
]
],
"rsquare_spl": [
[
{
"id": "NA12878"
},
"NA12878.rsquare.spl.txt.gz:md5,30a00f0b1de47fd63414d819b4304ded"
]
],
"versions": [
"versions.yml:md5,b6c06f9736c60f9f548c3c082b522025"
]
],
[
[
{
"id": "input"
},
"input.error.spl.txt.gz:md5,35cb463e8db41e2180f21941ab0324e0"
]
],
[
[
{
"id": "input"
},
"input.rsquare.spl.txt.gz:md5,55659f466775d828ee1ba723464bb460"
]
],
[
"versions.yml:md5,f79c864118d03a4afa93082c46c0d608"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-15T12:50:35.203335"
"timestamp": "2025-11-27T11:08:34.841155791"
}
}
5 changes: 5 additions & 0 deletions modules/nf-core/glimpse/concordance/tests/nextflow.config
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@@ -0,0 +1,5 @@
process {
withName: GLIMPSE_CONCORDANCE {
ext.args = "--gt-validation --gt-target"
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/glimpse/ligate/main.nf
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Expand Up @@ -22,7 +22,7 @@ process GLIMPSE_LIGATE {
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "vcf.gz"
"""
printf "%s\\n" $input_list | tr -d '[],' > all_files.txt
printf "%s\\n" $input_list | tr -d '[],' | sort -V > all_files.txt

GLIMPSE_ligate \\
$args \\
Expand All @@ -31,8 +31,8 @@ process GLIMPSE_LIGATE {
--output ${prefix}.${suffix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
glimpse: "\$(GLIMPSE_ligate --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
"${task.process}":
glimpse: "\$(GLIMPSE_ligate --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
END_VERSIONS
"""

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