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Updated test data paths batch40 (nf-core#6196)
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@GallVp
GallVp authored Aug 16, 2024
1 parent 61123e4 commit ab80a04
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Showing 5 changed files with 31 additions and 31 deletions.
8 changes: 4 additions & 4 deletions subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ nextflow_workflow {
input[0] = [
[ id:'test', single_end:false ], // meta map
[
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 All @@ -45,7 +45,7 @@ nextflow_workflow {
"""
input[0] = [
[ id:'sarscov2'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
"""
}
Expand All @@ -56,7 +56,7 @@ nextflow_workflow {
"""
input[0] = UMITOOLS_EXTRACT.out.reads
input[1] = BWA_INDEX.out.index
input[2] = [[ id:'sarscov2'],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
input[2] = [[ id:'sarscov2'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = true
"""
}
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34 changes: 17 additions & 17 deletions subworkflows/nf-core/bam_qc_picard/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,22 +18,22 @@ nextflow_workflow {
workflow {
"""
input[0] = Channel.of([ [ id:'test', single_end:false ],
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.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:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[2] = [
[id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
]
input[3] = [
[id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
]
"""
}
Expand Down Expand Up @@ -72,22 +72,22 @@ nextflow_workflow {
workflow {
"""
input[0] = Channel.of([ [ id:'test', single_end:false ],
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']['baits_interval_list'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
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/picard/baits.interval_list', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true)
])
input[1] = [
[id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[2] = [
[id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
]
input[3] = [
[id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
]
"""
}
Expand Down Expand Up @@ -129,22 +129,22 @@ nextflow_workflow {
workflow {
"""
input[0] = Channel.of([ [ id:'test', single_end:false ],
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.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:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[2] = [
[id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
]
input[3] = [
[id:'genome'],
file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
]
"""
}
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12 changes: 6 additions & 6 deletions subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,11 @@ nextflow_workflow {
input[0] = Channel.of(
[
[ 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)
],
[
[ id:'test2' ],
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] = Channel.of(
Expand Down Expand Up @@ -62,11 +62,11 @@ nextflow_workflow {
input[0] = Channel.of(
[
[ 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)
],
[
[ id:'test2' ],
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] = Channel.of(
Expand Down Expand Up @@ -97,11 +97,11 @@ nextflow_workflow {
input[0] = Channel.of(
[
[ 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)
],
[
[ id:'test2' ],
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] = []
Expand Down
6 changes: 3 additions & 3 deletions subworkflows/nf-core/fastq_align_mapad/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_workflow {
script "../../../../modules/nf-core/mapad/index/main.nf"
process {
"""
input[0] = [ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)]
input[0] = [ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
"""
}
}
Expand All @@ -30,11 +30,11 @@ nextflow_workflow {
workflow {
"""
input[0] = Channel.of([ [ id:'test', single_end:true ], // 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)
])
input[1] = MAPAD_INDEX.out.index
input[2] = [ [ id:'genome' ],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[3] = 0.03
input[4] = false
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/mmseqs_contig_taxonomy/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ nextflow_workflow {
"""
input[0] = Channel.of([
[id:'bacteroides_fragilis'],
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

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