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Updated test data paths batch41 (nf-core#6198)
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@GallVp
GallVp authored Aug 16, 2024
1 parent ab80a04 commit 0fa40bb
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Showing 3 changed files with 48 additions and 48 deletions.
24 changes: 12 additions & 12 deletions subworkflows/nf-core/fastq_align_bowtie2/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -19,19 +19,19 @@ nextflow_workflow {
script "../../../../modules/nf-core/bowtie2/build/main.nf"
process {
"""
input[0] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[0] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
}
when {
workflow {
"""
input[0] = Channel.of([[ id:'test', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]])
input[0] = Channel.of([[ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]])
input[1] = BOWTIE2_BUILD.out.index
input[2] = false
input[3] = false
input[4] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[4] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
Expand Down Expand Up @@ -61,19 +61,19 @@ nextflow_workflow {
script "../../../../modules/nf-core/bowtie2/build/main.nf"
process {
"""
input[0] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[0] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
}
when {
workflow {
"""
input[0] = Channel.of([[ id:'test', single_end:false ], [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 ], [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] = BOWTIE2_BUILD.out.index
input[2] = false
input[3] = false
input[4] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[4] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
Expand Down Expand Up @@ -106,19 +106,19 @@ nextflow_workflow {
script "../../../../modules/nf-core/bowtie2/build/main.nf"
process {
"""
input[0] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[0] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
}
when {
workflow {
"""
input[0] = Channel.of([[ id:'test', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]])
input[0] = Channel.of([[ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]])
input[1] = BOWTIE2_BUILD.out.index
input[2] = false
input[3] = false
input[4] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[4] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
Expand Down Expand Up @@ -151,19 +151,19 @@ nextflow_workflow {
script "../../../../modules/nf-core/bowtie2/build/main.nf"
process {
"""
input[0] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[0] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
}
when {
workflow {
"""
input[0] = Channel.of([[ id:'test', single_end:false ], [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 ], [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] = BOWTIE2_BUILD.out.index
input[2] = false
input[3] = false
input[4] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[4] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
Expand Down
12 changes: 6 additions & 6 deletions subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,18 +20,18 @@ nextflow_workflow {
script "../../../../modules/nf-core/bwa/index/main.nf"
process {
"""
input[0] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[0] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
}
when {
workflow {
"""
input[0] = Channel.of([[ id:'test', single_end:true ],[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]])
input[0] = Channel.of([[ id:'test', single_end:true ],[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]])
input[1] = BWA_INDEX.out.index
input[2] = false
input[3] = Channel.value([[id: 'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[3] = Channel.value([[id: 'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
Expand All @@ -50,19 +50,19 @@ nextflow_workflow {
script "../../../../modules/nf-core/bwa/index/main.nf"
process {
"""
input[0] = Channel.value([ [ id:'genome' ],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[0] = Channel.value([ [ id:'genome' ],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
}
when {
workflow {
"""
input[0] = Channel.of([[ id:'test', single_end:false ], [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 ], [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] = BWA_INDEX.out.index
input[2] = false
input[3] = Channel.value([[id: 'genome'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)])
input[3] = Channel.value([[id: 'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
"""
}
}
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