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CHORES: update fastp tests with new data organisation (nf-core#4758)
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update fastp tests with new data organisation
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@maxulysse
maxulysse authored Jan 17, 2024
1 parent 1b0ffa4 commit 1799e45
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Showing 2 changed files with 54 additions and 57 deletions.
95 changes: 46 additions & 49 deletions modules/nf-core/fastp/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,10 @@ nextflow_process {
save_trimmed_fail = false
save_merged = false
input[0] = [
input[0] = Channel.of([
[ id:'test', single_end:true ],
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -89,11 +88,10 @@ nextflow_process {
save_trimmed_fail = false
save_merged = false
input[0] = [
input[0] = Channel.of([
[ id:'test', single_end:true ],
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -135,12 +133,11 @@ nextflow_process {
save_trimmed_fail = false
save_merged = false
input[0] = [
input[0] = Channel.of([
[ 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) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -220,12 +217,11 @@ nextflow_process {
save_trimmed_fail = false
save_merged = false
input[0] = [
input[0] = Channel.of([
[ 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) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -266,10 +262,10 @@ nextflow_process {
save_trimmed_fail = false
save_merged = false
input[0] = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ]
]
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -336,10 +332,10 @@ nextflow_process {
save_trimmed_fail = false
save_merged = false
input[0] = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ]
]
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -380,9 +376,10 @@ nextflow_process {
save_trimmed_fail = true
save_merged = false
input[0] = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -440,13 +437,11 @@ nextflow_process {
save_trimmed_fail = true
save_merged = false
input[0] = [
input[0] = Channel.of([
[ 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)]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -519,11 +514,11 @@ nextflow_process {
adapter_fasta = []
save_trimmed_fail = false
save_merged = true
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) ]
]
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[ 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) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -613,10 +608,11 @@ nextflow_process {
save_trimmed_fail = false
save_merged = true
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) ]
]
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[ 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) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down Expand Up @@ -653,14 +649,15 @@ nextflow_process {
}
process {
"""
adapter_fasta = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta", checkIfExists: true)
adapter_fasta = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ])
save_trimmed_fail = false
save_merged = true
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) ]
]
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[ 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) ]
])
input[1] = adapter_fasta
input[2] = save_trimmed_fail
input[3] = save_merged
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/fastp/tests/main.nf.test.snap
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