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Updated test data paths batch 26 (#6146)
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@GallVp
GallVp authored Aug 9, 2024
1 parent 3549a36 commit a3d614e
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Showing 7 changed files with 29 additions and 29 deletions.
4 changes: 2 additions & 2 deletions modules/nf-core/bedtools/bamtobed/tests/main.nf.test
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Expand Up @@ -14,7 +14,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
]
"""
}
Expand All @@ -38,7 +38,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
]
"""
}
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18 changes: 9 additions & 9 deletions modules/nf-core/bedtools/closest/tests/main.nf.test
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Expand Up @@ -14,10 +14,10 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
[
file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
]
]
input[1] = []
Expand All @@ -40,10 +40,10 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
]
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
"""
}
}
Expand All @@ -63,10 +63,10 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
[
file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
]
]
input[1] = []
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4 changes: 2 additions & 2 deletions modules/nf-core/bedtools/complement/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@ nextflow_process {
"""
input[0] = [
[ id:'test_out' ], // meta map
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
]
input[1] = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
"""
}
}
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10 changes: 5 additions & 5 deletions modules/nf-core/bedtools/coverage/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
]
input[1] = []
"""
Expand All @@ -38,10 +38,10 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
]
input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
"""
}
}
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8 changes: 4 additions & 4 deletions modules/nf-core/bedtools/getfasta/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,10 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
]
input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
}
}
Expand All @@ -42,10 +42,10 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
]
input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
"""
}
}
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12 changes: 6 additions & 6 deletions modules/nf-core/bedtools/map/tests/main.nf.test
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Expand Up @@ -18,8 +18,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
]
input[1] = [[],[]]
"""
Expand All @@ -42,8 +42,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
]
input[1] = [[],[]]
"""
Expand All @@ -67,8 +67,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
]
input[1] = [[],[]]
"""
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2 changes: 1 addition & 1 deletion modules/nf-core/bedtools/merge/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 {
process {
"""
input[0] = [ [ id:'test'],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
]
"""
}
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