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Remove test_data usage #10029

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ce279a5
Modify test_data
Feb 13, 2026
7cce3c0
Update test data
Feb 13, 2026
bcc5551
Remove meta comment
Feb 13, 2026
ce268d9
Fix aria2
LouisLeNezet Feb 14, 2026
e34f34f
Fix test
LouisLeNezet Feb 14, 2026
17fc0a5
Fix test
LouisLeNezet Feb 14, 2026
6d7fe6b
Merge branch 'master' into test_data
LouisLeNezet Feb 14, 2026
8de82cd
Revert change graphtyper
LouisLeNezet Feb 14, 2026
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18 changes: 10 additions & 8 deletions modules/nf-core/aria2/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -10,16 +10,17 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
params.test_data['sarscov2']['illumina']['test_single_end_bam'] // https URL
]
input[0] = [
[ id:'test' ],
params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam'
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -29,16 +30,17 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test' ], // meta map
params.test_data['sarscov2']['illumina']['test_single_end_bam'] // https URL
]
input[0] = [
[ id:'test' ],
params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam'
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
34 changes: 10 additions & 24 deletions modules/nf-core/aria2/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,17 +2,6 @@
"sarscov2 Illumina single end [bam] - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.single_end.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,1d3d763f0ff390b632205a498112b076"
],
"downloaded_file": [
[
{
Expand All @@ -26,22 +15,15 @@
]
}
],
"timestamp": "2023-12-14T17:34:30.569759"
"timestamp": "2026-02-14T11:40:12.900794609",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"sarscov2 Illumina single end [bam]": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.single_end.bam:md5,21afed4c3e007de5e007cc5cbaebede7"
]
],
"1": [
"versions.yml:md5,1d3d763f0ff390b632205a498112b076"
],
"downloaded_file": [
[
{
Expand All @@ -55,6 +37,10 @@
]
}
],
"timestamp": "2023-12-14T17:34:22.216677"
"timestamp": "2026-02-14T11:40:06.798917586",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
}
}
24 changes: 12 additions & 12 deletions modules/nf-core/bcftools/consensus/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,10 @@ nextflow_process {
"""
input[0] = [
[ id:'test'],
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
]
"""
}
Expand All @@ -44,9 +44,9 @@ nextflow_process {
"""
input[0] = [
[ id:'test'],
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
[]
]
"""
Expand All @@ -70,11 +70,11 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
]
"""
}
Expand Down
19 changes: 13 additions & 6 deletions modules/nf-core/centrifuge/centrifuge/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,10 @@ nextflow_process {
when {
process {
"""
input[0] = [ [id: 'test', single_end: true], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
input[0] = [
[id: 'test', single_end: true],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
]
input[1] = UNTAR.out.untar.map{ it[1] }
input[2] = true
input[3] = true
Expand Down Expand Up @@ -54,10 +57,11 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
[id: 'test', single_end: false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)

]
input[1] = UNTAR.out.untar.map{ it[1] }
input[2] = true
input[3] = true
Expand Down Expand Up @@ -86,7 +90,10 @@ nextflow_process {
when {
process {
"""
input[0] = [ [id: 'test'], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
input[0] = [
[id: 'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
]
input[1] = UNTAR.out.untar.map{ it[1] }
input[2] = true
input[3] = true
Expand Down
5 changes: 4 additions & 1 deletion modules/nf-core/centrifuge/kreport/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,10 @@ nextflow_process {
script "../../../centrifuge/centrifuge/main.nf"
process {
"""
input[0] = [ [id: 'test', single_end: true], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
input[0] = [
[id: 'test', single_end: true],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
]
input[1] = UNTAR.out.untar.map{ it[1] }
input[2] = true
input[3] = true
Expand Down
20 changes: 8 additions & 12 deletions modules/nf-core/checkv/updatedatabase/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -34,12 +34,10 @@ nextflow_process {
}
process {
"""
input[0] = Channel.of(
[
[ id: 'test' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
)
input[0] = [
[ id: 'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = UNTAR.out.untar.map { it[1] }
"""
}
Expand Down Expand Up @@ -71,12 +69,10 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of(
[
[ id: 'test' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
)
input[0] = [
[ id: 'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = UNTAR.out.untar.map { it[1] }
"""
}
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/decoupler/decoupler/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -73,11 +73,11 @@ nextflow_process {
"""
input[0] = [
[ id: 'test', 'method_differential':'deseq2'],
file(params.test_data['generic']['tsv']['expression'], checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true)
]
input[1] = [
['id':'network'],
file(params.test_data['generic']['tsv']['network'], checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true)
]
input[2] = [
['id':'annot'],
Expand Down Expand Up @@ -126,11 +126,11 @@ nextflow_process {
"""
input[0] = [
[ id: 'test' ],
file(params.test_data['generic']['tsv']['expression'], checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true)
]
input[1] = [
['id':'network'],
file(params.test_data['generic']['tsv']['network'], checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true)
]
input[2] = [
['id':'annot'],
Expand Down
24 changes: 4 additions & 20 deletions modules/nf-core/falco/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,7 @@ nextflow_process {
"""
input[0] = [
[ id: 'test', single_end:true ],
[
file(
params.test_data['sarscov2']['illumina']['test_1_fastq_gz'],
checkIfExists: true
),
],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
]
"""
}
Expand All @@ -47,14 +42,8 @@ nextflow_process {
input[0] = [
[ id: 'test', single_end:false ],
[
file(
params.test_data['sarscov2']['illumina']['test_1_fastq_gz'],
checkIfExists: true
),
file(
params.test_data['sarscov2']['illumina']['test_2_fastq_gz'],
checkIfExists: true
),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
],
]
"""
Expand All @@ -81,12 +70,7 @@ nextflow_process {
"""
input[0] = [
[ id: 'test', single_end:false ],
[
file(
params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'],
checkIfExists: true
),
],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)],
]
"""
}
Expand Down
10 changes: 5 additions & 5 deletions modules/nf-core/fast2q/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test1' ], // meta map
file(params.test_data_base + '/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file
]
input[1] = [
[ id:'library_name', multiple_features_per_read:false ], // meta map for second input
Expand Down Expand Up @@ -99,12 +99,12 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test1' ], // meta map
file(params.test_data_base + '/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file
[ id:'test1' ],
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file
]
input[1] = [
[ id:'library_name', multiple_features_per_read:false ], // meta map for second input
file(params.test_data_base + '/data/genomics/mus_musculus/mageck/yusa_library.csv', checkIfExists: true) // library file
[ id:'library_name', multiple_features_per_read:false ],
file(params.modules_testdata_base_path + 'genomics/mus_musculus/mageck/yusa_library.csv', checkIfExists: true) // library file
]
"""
}
Expand Down
15 changes: 9 additions & 6 deletions modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,13 @@ nextflow_process {
script "../../../bowtie2/build/main.nf"
process {
"""
input[0] = Channel.from([
[[id: "sarscov2"], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
[[id: "human"] , file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
])
input[0] = channel.of([
[id: "sarscov2"],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
], [
[id: "human"],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
])
"""
}
}
Expand All @@ -40,7 +43,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.database, process.out.versions).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -62,7 +65,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand Down
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