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Updated test data paths batch 6 #6060

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merged 3 commits into from
Jul 30, 2024
Merged

Updated test data paths batch 6 #6060

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1aa8172
Updated test data paths batch 6
GallVp Jul 30, 2024
862c538
Update main.nf
SPPearce Jul 30, 2024
b22675d
Merge branch 'master' into testpaths/batch6
SPPearce Jul 30, 2024
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6 changes: 3 additions & 3 deletions modules/nf-core/cutadapt/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ 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 Down Expand Up @@ -47,8 +47,8 @@ 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 Down
2 changes: 1 addition & 1 deletion modules/nf-core/gt/gff3/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_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
]
"""
}
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/gt/gff3validator/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,13 @@ nextflow_process {

setup {
run("GT_GFF3") {
script "../../../../nf-core/gt/gff3"
script "../../../gt/gff3"

process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
]
"""
}
Expand All @@ -40,9 +40,9 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert path(process.out.success_log[0][1]).text.contains("input is valid GFF3") },
{ assert process.out.error_log == [] }
{ assert process.out.error_log == [] },
{ assert snapshot(process.out).match() },
)
}

Expand All @@ -57,7 +57,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
]
"""
}
Expand All @@ -79,7 +79,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_gff3'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gff3', checkIfExists: true)
]
"""
}
Expand All @@ -88,9 +88,9 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert path(process.out.error_log[0][1]).text.contains("gt gff3validator: error:") },
{ assert process.out.success_log == [] },
{ assert path(process.out.error_log[0][1]).text.contains("gt gff3validator: error:") }
{ assert snapshot(process.out).match() },
)
}

Expand Down
25 changes: 10 additions & 15 deletions modules/nf-core/gt/ltrharvest/tests/main.nf.test
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
input[1] = 'dna'
"""
Expand All @@ -40,8 +40,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(process.out).match() }
)
}

Expand All @@ -59,7 +58,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
input[1] = 'dna'
"""
Expand All @@ -78,8 +77,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(process.out).match() }
)
}

Expand All @@ -97,7 +95,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
input[1] = 'dna'
"""
Expand All @@ -116,8 +114,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(process.out).match() }
)
}

Expand All @@ -132,7 +129,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
"""
}
Expand All @@ -141,8 +138,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(process.out).match() }
)
}

Expand All @@ -158,7 +154,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
]
"""
}
Expand All @@ -167,8 +163,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(process.out).match() }
)
}

Expand Down
46 changes: 19 additions & 27 deletions modules/nf-core/gt/ltrharvest/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -11,25 +11,25 @@
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
"versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
],
"fasta": [

],
"gff3": [

],
"inner_fasta": [

],
"tabout": [
[
Expand All @@ -46,14 +46,6 @@
],
"timestamp": "2024-01-16T09:42:10.114754"
},
"versions": {
"content": [
[
"versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
]
],
"timestamp": "2024-01-17T11:12:11.954224"
},
"stub": {
"content": [
{
Expand All @@ -66,25 +58,25 @@
]
],
"1": [

],
"2": [

],
"3": [

],
"4": [
"versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
],
"fasta": [

],
"gff3": [

],
"inner_fasta": [

],
"tabout": [
[
Expand All @@ -105,7 +97,7 @@
"content": [
{
"0": [

],
"1": [
[
Expand Down Expand Up @@ -159,7 +151,7 @@
]
],
"tabout": [

],
"versions": [
"versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
Expand All @@ -172,7 +164,7 @@
"content": [
{
"0": [

],
"1": [
[
Expand Down Expand Up @@ -226,7 +218,7 @@
]
],
"tabout": [

],
"versions": [
"versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
Expand All @@ -239,7 +231,7 @@
"content": [
{
"0": [

],
"1": [
[
Expand Down Expand Up @@ -293,7 +285,7 @@
]
],
"tabout": [

],
"versions": [
"versions.yml:md5,8df72f2f0252e314180bde73e0bbae37"
Expand All @@ -302,4 +294,4 @@
],
"timestamp": "2024-01-17T11:20:13.665071"
}
}
}
4 changes: 2 additions & 2 deletions modules/nf-core/gt/stat/tests/main.nf.test
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ nextflow_process {
"""
input[0] = Channel.of(
"##gff-version 3" +
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true).text.toLowerCase()
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true).text.toLowerCase()
)
.collectFile(name: 'sample.gff3', newLine: true)
.map { file -> [ [ id:'test' ], file ] }
Expand All @@ -43,7 +43,7 @@ nextflow_process {
"""
input[0] = [
[ id: 'test' ],
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
]
"""
}
Expand Down
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