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Fix test path modification #9465

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e9c0c7f
Update bcftools
Nov 26, 2025
9a3d9c9
Update bcftools csq
Nov 26, 2025
56daf9d
Update somalier ancestry
Nov 26, 2025
4455bb6
Update bcftools pluginfilltags
Nov 26, 2025
af1f47f
Update cnvnator
Nov 26, 2025
fd64e5b
Update snap cnvnator
Nov 26, 2025
707d125
Fix extract somalier sbwf
Nov 26, 2025
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68 changes: 34 additions & 34 deletions modules/nf-core/bcftools/concat/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand All @@ -50,12 +50,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand Down Expand Up @@ -87,12 +87,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand Down Expand Up @@ -124,12 +124,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand Down Expand Up @@ -162,8 +162,8 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[]
]
Expand Down Expand Up @@ -191,12 +191,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand All @@ -223,12 +223,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand Down Expand Up @@ -256,12 +256,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand Down Expand Up @@ -289,12 +289,12 @@ nextflow_process {
input[0] = [
[ id:'test3' ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
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_GIAB.chr21_22.vcf.gz', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
]
]
"""
Expand Down
44 changes: 22 additions & 22 deletions modules/nf-core/bcftools/concat/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
{
"id": "test3"
},
"test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6"
"test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
]
],
[
Expand All @@ -25,10 +25,10 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-15T11:26:25.259752"
"timestamp": "2025-11-26T16:53:25.503018154"
},
"homo_sapiens - [[vcf1, vcf2], []]": {
"content": [
Expand All @@ -38,7 +38,7 @@
{
"id": "test3"
},
"test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
"test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
]
],
"1": [
Expand All @@ -61,7 +61,7 @@
{
"id": "test3"
},
"test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
"test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
]
],
"versions": [
Expand All @@ -70,10 +70,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-15T10:03:17.250013"
"timestamp": "2025-11-26T16:56:01.364652383"
},
"homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
"content": [
Expand Down Expand Up @@ -182,7 +182,7 @@
{
"id": "test3"
},
"test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6"
"test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
]
],
[
Expand All @@ -201,10 +201,10 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-15T11:26:31.742638"
"timestamp": "2025-11-26T16:53:33.38516503"
},
"homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": {
"content": [
Expand All @@ -214,7 +214,7 @@
{
"id": "test3"
},
"test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
"test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
]
],
"1": [
Expand All @@ -237,7 +237,7 @@
{
"id": "test3"
},
"test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
"test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
]
],
"versions": [
Expand All @@ -246,10 +246,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-15T10:29:33.203302"
"timestamp": "2025-11-26T16:55:30.850726912"
},
"homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": {
"content": [
Expand All @@ -258,7 +258,7 @@
{
"id": "test3"
},
"test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6"
"test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
]
],
[
Expand All @@ -277,10 +277,10 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-15T11:26:17.482474"
"timestamp": "2025-11-26T16:53:18.091429133"
},
"homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": {
"content": [
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/bcftools/concat/tests/nextflow.config
View file
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
process {
ext.args = "--no-version"
ext.args = "--no-version -a"
}
2 changes: 1 addition & 1 deletion modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config
View file
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
process {
ext.prefix = { "${meta.id}_vcf" }
ext.args = "--output-type z --write-index=csi --no-version --allow-overlaps"
ext.args = "--output-type z --write-index=csi --no-version --allow-overlaps -a"
}
2 changes: 1 addition & 1 deletion modules/nf-core/bcftools/csq/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
]
input[1] = [
[ : ], // meta map
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/bcftools/csq/tests/main.nf.test.snap
View file
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Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
{
"homo_sapiens": {
"content": [
"876b0b2fe3971805ff1d546775efe5f",
"a048c8564339aa411b019310f5a84326",
[
"versions.yml:md5,05afacd9179e80fd0d23218033c3aca9"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-15T12:03:18.948435"
"timestamp": "2025-11-26T16:58:26.677826042"
}
}
8 changes: 4 additions & 4 deletions modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ nextflow_process {
"""
input[0] = Channel.of([
[id:'NA12878', region:"chr22:16570065-16609999"],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz", checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi", checkIfExists: true),
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),
])
input[1] = []
input[2] = []
Expand Down Expand Up @@ -119,8 +119,8 @@ nextflow_process {
"""
input[0] = Channel.of([
[id:'NA12878', region:"chr22:16570065-16609999"],
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz", checkIfExists: true),
file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi", checkIfExists: true),
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),
])
input[1] = []
input[2] = []
Expand Down
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