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Use global SETUP for making index for STAR_ALIGN tests (#4871)
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* Use global SETUP for making index for STAR_ALIGN tests

* CHORES: Update STAR_GENOMEGENERATE modules to use path rather than map
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@adamrtalbot
adamrtalbot authored Feb 12, 2024
1 parent 220da1a commit a21faa6
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140 changes: 34 additions & 106 deletions modules/nf-core/star/align/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -9,38 +9,38 @@ nextflow_process {
tag "star/align"
tag "star/genomegenerate"

test("homo_sapiens - single_end") {
config "./nextflow.config"

setup {
run("STAR_GENOMEGENERATE") {
script "../../../star/genomegenerate/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
])
"""
}
setup {
run("STAR_GENOMEGENERATE") {
script "../../../star/genomegenerate/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
"""
}
}
}

test("homo_sapiens - single_end") {
config "./nextflow.config"

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
Expand Down Expand Up @@ -75,38 +75,20 @@ nextflow_process {
test("homo_sapiens - paired_end") {
config "./nextflow.config"

setup {
run("STAR_GENOMEGENERATE") {
script "../../../star/genomegenerate/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
])
"""
}
}
}

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
Expand Down Expand Up @@ -141,38 +123,20 @@ nextflow_process {
test("homo_sapiens - paired_end - arriba") {
config "./nextflow.arriba.config"

setup {
run("STAR_GENOMEGENERATE") {
script "../../../star/genomegenerate/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
])
"""
}
}
}

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
Expand Down Expand Up @@ -207,38 +171,20 @@ nextflow_process {
test("homo_sapiens - paired_end - starfusion") {
config "./nextflow.starfusion.config"

setup {
run("STAR_GENOMEGENERATE") {
script "../../../star/genomegenerate/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
])
"""
}
}
}

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
Expand Down Expand Up @@ -273,40 +219,22 @@ nextflow_process {
test("homo_sapiens - paired_end - multiple") {
config "./nextflow.config"

setup {
run("STAR_GENOMEGENERATE") {
script "../../../star/genomegenerate/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
])
"""
}
}
}

when {
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-core/star/genomegenerate/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,11 @@ nextflow_process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[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) ]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
"""
}
Expand All @@ -43,11 +43,11 @@ nextflow_process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[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) ]
])
input[1] = Channel.of([
[ id:'test_gtf' ],
[file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)]
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
"""
}
Expand All @@ -69,7 +69,7 @@ nextflow_process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[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) ]
])
input[1] = Channel.of([ [], [] ])
"""
Expand All @@ -95,7 +95,7 @@ nextflow_process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[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) ]
])
input[1] = Channel.of([ [], [] ])
"""
Expand Down

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