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Updated test data paths batch 16 (#6102)
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Updated paths
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@GallVp
GallVp authored Aug 3, 2024
1 parent 4ba1155 commit 9837ac7
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Showing 10 changed files with 32 additions and 32 deletions.
4 changes: 2 additions & 2 deletions modules/nf-core/abricate/run/tests/main.nf.test
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Expand Up @@ -18,7 +18,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
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)
]
input[1] = []
"""
Expand All @@ -45,7 +45,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
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)
]
input[1] = []
"""
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4 changes: 2 additions & 2 deletions modules/nf-core/abricate/summary/meta.yml
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Expand Up @@ -17,7 +17,7 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- assembly:
- reports:
type: file
description: FASTA, GenBank or EMBL formatted file
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
Expand All @@ -31,7 +31,7 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- summary:
- report:
type: file
description: Tab-delimited report of aggregated results
pattern: "*.{txt}"
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4 changes: 2 additions & 2 deletions modules/nf-core/abricate/summary/tests/main.nf.test
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Expand Up @@ -18,9 +18,9 @@ nextflow_process {
"""
input[0] = Channel.fromList([
tuple([ id:'test1', single_end:false ], // meta map
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)),
tuple([ id:'test2', single_end:false ],
file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true))
])
input[1] = []
"""
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32 changes: 16 additions & 16 deletions modules/nf-core/angsd/gl/tests/main.nf.test
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Expand Up @@ -18,11 +18,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
Expand All @@ -46,11 +46,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
Expand All @@ -74,11 +74,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
Expand All @@ -102,11 +102,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
Expand All @@ -132,11 +132,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
Expand All @@ -162,11 +162,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
Expand All @@ -192,11 +192,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
Expand All @@ -222,11 +222,11 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
]
input[1] = [
[ id:'test_fa' ],
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[2] = [ [], [] ]
"""
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2 changes: 1 addition & 1 deletion modules/nf-core/bacphlip/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']['genome_fasta'], checkIfExists: true) // genome.fasta
file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta', checkIfExists: true) // genome.fasta
]
"""
}
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4 changes: 2 additions & 2 deletions modules/nf-core/cellpose/tests/main.nf.test
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Expand Up @@ -16,7 +16,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['imaging']['segmentation']['image'], checkIfExists: true)
file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true)
]
input[1] = []
"""
Expand Down Expand Up @@ -44,7 +44,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test' ],
file(params.test_data['imaging']['segmentation']['image'], checkIfExists: true)
file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true)
]
input[1] = []
"""
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4 changes: 2 additions & 2 deletions modules/nf-core/hamronization/abricate/tests/main.nf.test
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Expand Up @@ -14,7 +14,7 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:"test" ], file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true) ]
input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ]
input[1] = 'tsv'
input[2] = '1.0.1'
input[3] = '2021-Mar-27'
Expand All @@ -37,7 +37,7 @@ nextflow_process {
when {
process {
"""
input[0] = [ [ id:"test" ], file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true) ]
input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ]
input[1] = 'tsv'
input[2] = '1.0.1'
input[3] = '2021-Mar-27'
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4 changes: 2 additions & 2 deletions modules/nf-core/hamronization/deeparg/tests/main.nf.test
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Expand Up @@ -16,7 +16,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true),
]
input[1] = 'tsv'
input[2] = '1.0.2'
Expand All @@ -43,7 +43,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true),
]
input[1] = 'tsv'
input[2] = '1.0.2'
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/hamronization/fargene/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ nextflow_process {
"""
input[0] = Channel.fromList([
tuple([ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true))
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true))
])
"""
}
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/hamronization/summarize/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test1', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true),
]
input[1] = 'tsv'
input[2] = '1.0.2'
Expand All @@ -32,7 +32,7 @@ nextflow_process {
"""
input[0] = [
[ id:'test2', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG', checkIfExists: true),
]
input[1] = 'tsv'
input[2] = '1.0.2'
Expand Down

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