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main.nf.test
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109 lines (100 loc) · 3.9 KB
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nextflow_process {
name "Test Process BCLCONVERT"
script "../main.nf"
process "BCLCONVERT"
config "./nextflow.config"
tag "bclconvert"
tag "modules"
tag "modules_nfcore"
test("homo_sapiens illumina [bcl]") {
when {
params {
module_args = "--force --first-tile-only true"
}
process {
"""
input[0] = [
[ id: 'test', lane:1 ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.fastq_idx,
process.out.undetermined.collect { meta, fastq -> file(fastq).name },
process.out.undetermined_idx,
process.out.reports.collect {meta, dir -> file(dir).name },
process.out.logs.collect {meta, dir -> file(dir).name },
process.out.interop.collect {meta, files -> files.collect { file(it).name }.sort() },
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
}
test("sars_cov2 illumina [bcl]") {
when {
params {
module_args = "--force --tiles s_1_2101"
}
process {
"""
input[0] = [
[ id: 'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bcl/SampleSheet.csv', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bcl/200624_A00834_0183_BHMTFYDRXX.tar.gz', checkIfExists: true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq.collect {
meta, fastqs ->
fastqs.findAll {
fastqfile ->
file(fastqfile).name != "SampleZ_S5_L001_R1_001.fastq.gz"
}
},
process.out.fastq_idx,
process.out.undetermined.collect { meta, fastq -> file(fastq).name },
process.out.undetermined_idx,
process.out.reports.collect {meta, dir -> file(dir).name },
process.out.logs.collect {meta, dir -> file(dir).name },
process.out.interop.collect {meta, files -> files.collect { file(it).name }.sort() },
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
}
test("homo_sapiens illumina [bcl] - stub") {
options "-stub"
when {
params {
module_args = "--force --first-tile-only true"
}
process {
"""
input[0] = [
[ id: 'test', lane:1 ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}