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Updated data paths
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@GallVp
GallVp committed Aug 1, 2024
1 parent 90dad54 commit 00d88bb
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Showing 9 changed files with 84 additions and 84 deletions.
4 changes: 2 additions & 2 deletions modules/nf-core/ampir/tests/main.nf.test
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Expand Up @@ -15,7 +15,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true),
]
input[1] = "precursor" // model
input[2] = 10 // min_length
Expand All @@ -42,7 +42,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true),
]
input[1] = "precursor" // model
input[2] = 10 // min_length
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90 changes: 45 additions & 45 deletions modules/nf-core/bowtie2/align/tests/main.nf.test
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2 changes: 1 addition & 1 deletion modules/nf-core/checkm2/predict/tests/main.nf.test
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Expand Up @@ -23,7 +23,7 @@ nextflow_process {
}
process {
"""
input[0] = [ [id: 'test'], [file(params.test_data['sarscov2']['illumina']['contigs_fasta'])] ]
input[0] = [ [id: 'test'], [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)] ]
input[1] = CHECKM2_DATABASEDOWNLOAD.out.database
"""
}
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6 changes: 3 additions & 3 deletions modules/nf-core/fcs/fcsadaptor/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' ],
file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
"""
}
Expand Down Expand Up @@ -44,7 +44,7 @@ nextflow_process {
when {
process {
"""
def input_file_lines = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true).text.split('\\n')
def input_file_lines = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true).text.split('\\n')
def file_with_adapters = file('sarscov2_with_adapters.fasta')
file_with_adapters.text = (
input_file_lines[0..<(input_file_lines.size()/2)]
Expand Down Expand Up @@ -89,7 +89,7 @@ nextflow_process {
"""
input[0] = [
[ id: 'test' ],
file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
"""
}
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4 changes: 2 additions & 2 deletions modules/nf-core/foldseek/createdb/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ nextflow_process {
when {
process {
"""
input[0] = [ [id:'test'], file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ]
input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ]
"""
}
}
Expand All @@ -34,7 +34,7 @@ nextflow_process {
when {
process {
"""
input[0] = [ [id:'test'], file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ]
input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ]
"""
}
}
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6 changes: 3 additions & 3 deletions modules/nf-core/foldseek/easysearch/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ nextflow_process {
script "../../createdb/main.nf"
process {
"""
input[0] = [ [ id:'test_db' ], [ file(params.test_data['proteomics']['pdb']['tim1_pdb'], checkIfExists: true) ] ]
input[0] = [ [ id:'test_db' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/1tim.pdb', checkIfExists: true) ] ]
"""
}
}
Expand All @@ -25,7 +25,7 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test_search' ], [ file(params.test_data['proteomics']['pdb']['tim8_pdb'], checkIfExists: true) ] ]
input[0] = [ [ id:'test_search' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/8tim.pdb', checkIfExists: true) ] ]
input[1] = FOLDSEEK_CREATEDB.out.db
"""
}
Expand All @@ -48,7 +48,7 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:'test_search' ], [ file(params.test_data['proteomics']['pdb']['tim8_pdb'], checkIfExists: true) ] ]
input[0] = [ [ id:'test_search' ], [ file(params.modules_testdata_base_path + 'proteomics/pdb/8tim.pdb', checkIfExists: true) ] ]
input[1] = FOLDSEEK_CREATEDB.out.db
"""
}
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4 changes: 2 additions & 2 deletions modules/nf-core/isoseq3/tag/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ nextflow_process {
"""
input[0] = [
[ id:'mini'], // meta map
file(params.test_data['homo_sapiens']['pacbio']['tag'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam', checkIfExists: true)
]
input[1] = "T-12U-16B"
"""
Expand Down Expand Up @@ -44,7 +44,7 @@ nextflow_process {
"""
input[0] = [
[ id:'mini'], // meta map
file(params.test_data['homo_sapiens']['pacbio']['tag'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/mini.5p--3p.bam', checkIfExists: true)
]
input[1] = "T-12U-16B"
"""
Expand Down
50 changes: 25 additions & 25 deletions modules/nf-core/mosdepth/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:true ],
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),
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),
[]
]
input[1] = [[],[]]
Expand All @@ -40,9 +40,9 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
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),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
]
input[1] = [[],[]]
"""
Expand All @@ -65,13 +65,13 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[]
]
input[1] = [
[ id:'test' ],
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
"""
}
Expand All @@ -93,13 +93,13 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
]
input[1] = [
[ id:'test' ],
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
"""
}
Expand All @@ -122,8 +122,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
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),
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),
[]
]
input[1] = [[],[]]
Expand All @@ -148,8 +148,8 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
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),
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),
[]
]
input[1] = [[],[]]
Expand All @@ -174,9 +174,9 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
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),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
]
input[1] = [[],[]]
"""
Expand All @@ -200,9 +200,9 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
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),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
]
input[1] = [[],[]]
"""
Expand All @@ -225,9 +225,9 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:true ],
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),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
]
input[1] = [[],[]]
"""
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/stringtie/merge/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ nextflow_process {
process {
"""
input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] }
input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)
"""
}
}
Expand Down

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