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Updated test data paths batch42 (nf-core#6199)
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@GallVp
GallVp authored Aug 16, 2024
1 parent 0fa40bb commit e4e61bf
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Showing 11 changed files with 171 additions and 116 deletions.
17 changes: 9 additions & 8 deletions modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,9 @@ nextflow_process {
script "../../preprocessintervals/main.nf"
process {
"""
input[0] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)])
input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)])
input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)])
input[0] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)])
input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)])
input[3] = [[],[]]
input[4] = [[],[]]
"""
Expand All @@ -33,12 +33,12 @@ nextflow_process {
"""
intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map {meta, list -> list}
input[0] = Channel.of(
[[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)],
[[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)],
)
.combine( intervals)
input[1] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)])
input[2] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)])
input[3] = Channel.value([ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)])
input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)])
input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)])
"""
}
}
Expand Down Expand Up @@ -66,7 +66,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.standardized,
process.out.denoised
process.out.denoised,
process.out.versions
).match() }
)
}
Expand Down
7 changes: 5 additions & 2 deletions modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,15 @@
},
"test_denoisedCR.tsv:md5,f9e56b8e12b4dadc91a6d977fa79c6a8"
]
],
[
"versions.yml:md5,140780e1af7318cc9259b8970bc70c81"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-02-20T14:45:41.834159"
"timestamp": "2024-08-16T12:34:12.568925"
}
}
48 changes: 27 additions & 21 deletions modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,10 @@ nextflow_process {
when {
process {
"""
input[0] = [[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), []]
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), []]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
input[4] = []
input[5] = []
"""
Expand All @@ -27,9 +27,11 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.vcf.get(0).get(1)).name,
file(process.out.vcf.get(0).get(2)).name
).match("test_gatk4_reblockgvcf") }
file(process.out.vcf[0][1]).name,
file(process.out.vcf[0][2]).name,
process.out.versions
).match()
}
)
}

Expand All @@ -39,10 +41,10 @@ nextflow_process {
when {
process {
"""
input[0] = [[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
input[4] = []
input[5] = []
"""
Expand All @@ -53,9 +55,11 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.vcf.get(0).get(1)).name,
file(process.out.vcf.get(0).get(2)).name
).match("test_gatk4_reblockgvcf_intervals") }
file(process.out.vcf[0][1]).name,
file(process.out.vcf[0][2]).name,
process.out.versions
).match()
}
)
}

Expand All @@ -68,10 +72,10 @@ nextflow_process {
when {
process {
"""
input[0] = [[ id:'test', single_end:false ], file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), []]
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
input[0] = [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), []]
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
input[4] = []
input[5] = []
"""
Expand All @@ -82,9 +86,11 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.vcf.get(0).get(1)).name,
file(process.out.vcf.get(0).get(2)).name
).match("test_gatk4_reblockgvcf_stub") }
file(process.out.vcf[0][1]).name,
file(process.out.vcf[0][2]).name,
process.out.versions
).match()
}
)
}

Expand Down
27 changes: 18 additions & 9 deletions modules/nf-core/gatk4/reblockgvcf/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,34 +2,43 @@
"test_gatk4_reblockgvcf_stub": {
"content": [
"test.rb.g.vcf.gz",
"test.rb.g.vcf.gz.tbi"
"test.rb.g.vcf.gz.tbi",
[
"versions.yml:md5,31df4173620cc2fbcca52d71f554015b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-02-14T15:38:51.810662542"
"timestamp": "2024-08-16T12:32:19.353113"
},
"test_gatk4_reblockgvcf_intervals": {
"content": [
"test.rb.g.vcf.gz",
"test.rb.g.vcf.gz.tbi"
"test.rb.g.vcf.gz.tbi",
[
"versions.yml:md5,31df4173620cc2fbcca52d71f554015b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-02-14T15:38:29.970623625"
"timestamp": "2024-08-16T12:32:11.896391"
},
"test_gatk4_reblockgvcf": {
"content": [
"test.rb.g.vcf.gz",
"test.rb.g.vcf.gz.tbi"
"test.rb.g.vcf.gz.tbi",
[
"versions.yml:md5,31df4173620cc2fbcca52d71f554015b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-02-14T15:38:01.110199615"
"timestamp": "2024-08-16T12:32:00.687676"
}
}
42 changes: 27 additions & 15 deletions modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,18 +14,22 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), []]
input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), []]
input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads") }
{ assert snapshot(
file(process.out.bam[0][1]).name,
process.out.versions
).match()
}
)
}

Expand All @@ -36,18 +40,22 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)]
input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_intervals") }
{ assert snapshot(
file(process.out.bam[0][1]).name,
process.out.versions
).match()
}
)
}

Expand All @@ -60,18 +68,22 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), [], []]
input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [], []]
input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ]
input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_stub") }
{ assert snapshot(
file(process.out.bam[0][1]).name,
process.out.versions
).match()
}
)
}

Expand Down
27 changes: 18 additions & 9 deletions modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,32 +1,41 @@
{
"test_gatk4_splitncigarreads_intervals": {
"content": [
"test.bam"
"test.bam",
[
"versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-02-15T08:26:10.91960579"
"timestamp": "2024-08-16T12:29:41.948726"
},
"test_gatk4_splitncigarreads_stub": {
"content": [
"test.bam"
"test.bam",
[
"versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-02-15T08:26:32.322712467"
"timestamp": "2024-08-16T12:29:53.2252"
},
"test_gatk4_splitncigarreads": {
"content": [
"test.bam"
"test.bam",
[
"versions.yml:md5,52030c97dd7da1d3e0df9475cc3f67cb"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-02-15T08:25:53.532205456"
"timestamp": "2024-08-16T12:29:30.774423"
}
}
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