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UMICollapse module: Drop external dependencies from UMICollapse module tests #7075

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UMICollapse module: Drop external dependencies from UMICollapse module tests #7075

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1a46557
Update the umi-tools dedup tests to use the new test data with UMIs.
MatthiasZepper Nov 23, 2024
4f2a5b8
Update umicollapse tests to use the new UMI test data.
MatthiasZepper Nov 24, 2024
f10e8fa
Switch to nf-bam plugin for output validation.
MatthiasZepper Nov 25, 2024
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226 changes: 77 additions & 149 deletions modules/nf-core/umicollapse/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -7,63 +7,18 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "umicollapse"
tag "umitools/extract"
tag "samtools/index"
tag "bwa/index"
tag "bwa/mem"

test("umicollapse single end test") {
setup{
run("UMITOOLS_EXTRACT"){
script "../../umitools/extract/main.nf"
config "./nextflow_SE.config"
process{
"""
input[0] = [
[ id:'test', single_end:true ], // 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)
]
]
"""
}
}

run("BWA_INDEX"){
script "../../bwa/index/main.nf"
process{
"""
input[0] = [[ id:'sarscov2'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
"""
}
}
run("BWA_MEM"){
script "../../bwa/mem/main.nf"
process{
"""
input[0] = UMITOOLS_EXTRACT.out.reads
input[1] = BWA_INDEX.out.index
input[2] = [[ id:'sarscov2'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = true
"""
}
}
run("SAMTOOLS_INDEX"){
script "../../samtools/index/main.nf"
process{
"""
input[0] = BWA_MEM.out.bam
"""
}
}
}

when {
config "./nextflow_SE.config"
config "./nextflow.config"
process {
"""
input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0])
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.umi.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.umi.sorted.bam.bai', checkIfExists: true)
])
input[1] = 'bam'
"""
}
Expand All @@ -73,68 +28,24 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.bam,
bam(process.out.bam[0][1]).getSamLinesMD5(),
process.out.versions).match() }
)
}

}

test("umicollapse paired tests") {
setup{
run("UMITOOLS_EXTRACT"){
script "../../umitools/extract/main.nf"
config "./nextflow_PE.config"
process{
"""
input[0] = [
[ 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)
]
]
"""
}
}

run("BWA_INDEX"){
script "../../bwa/index/main.nf"
process{
"""
input[0] = [
[ id:'sarscov2'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
"""
}
}
run("BWA_MEM"){
script "../../bwa/mem/main.nf"
process{
"""
input[0] = UMITOOLS_EXTRACT.out.reads
input[1] = BWA_INDEX.out.index
input[2] = [[ id:'sarscov2'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = true
"""
}
}
run("SAMTOOLS_INDEX"){
script "../../samtools/index/main.nf"
process{
"""
input[0] = BWA_MEM.out.bam
"""
}
}
}

when {
config "./nextflow_PE.config"
config "./nextflow.config"
process {
"""
input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0])
input[0] = Channel.of([
[ id:'test'], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.umi.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.umi.sorted.bam.bai', checkIfExists: true)
])
input[1] = 'bam'
"""
}
Expand All @@ -144,22 +55,22 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.bam,
bam(process.out.bam[0][1]).getSamLinesMD5(),
process.out.versions).match() }
)
}

}

test("umicollapse fastq tests") {
test("umicollapse fastq test (single-end)") {

when {
config "./nextflow_SE.config"
config "./nextflow.config"
process {
"""
input[0] = [
[ id:'test', single_end:true ], // 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.umi_extract_single.fastq.gz', checkIfExists: true),
[]
]
input[1] = 'fastq'
Expand All @@ -177,61 +88,76 @@ nextflow_process {
}
}

test("umicollapse stub tests") {
options "-stub-run"
setup{
run("UMITOOLS_EXTRACT"){
script "../../umitools/extract/main.nf"
config "./nextflow_PE.config"
process{
test("umicollapse fastq test (paired-end)") {

when {
config "./nextflow.config"
process {
"""
input[0] = [
[ 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)
]
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.umi_extract_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.umi_extract_2.fastq.gz', checkIfExists: true)
]
input[1] = 'fastq'
"""
}
}

run("BWA_INDEX"){
script "../../bwa/index/main.nf"
process{
"""
input[0] = [
[ id:'sarscov2'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
"""
}
}
run("BWA_MEM"){
script "../../bwa/mem/main.nf"
process{
"""
input[0] = UMITOOLS_EXTRACT.out.reads
input[1] = BWA_INDEX.out.index
input[2] = [[ id:'sarscov2'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = true
"""
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.versions).match() }
)
}
run("SAMTOOLS_INDEX"){
script "../../samtools/index/main.nf"
process{
"""
input[0] = BWA_MEM.out.bam
"""
}
}

// Stub tests

test("umicollapse single end test - stub") {

options "-stub"

when {
config "./nextflow.config"
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.umi.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.umi.sorted.bam.bai', checkIfExists: true)
])
input[1] = 'bam'
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions).match() }
)
}

}

test("umicollapse paired tests - stub") {

options "-stub"

when {
config "./nextflow_PE.config"
config "./nextflow.config"
process {
"""
input[0] = BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0])
input[0] = Channel.of([
[ id:'test'], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.umi.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.umi.sorted.bam.bai', checkIfExists: true)
])
input[1] = 'bam'
"""
}
Expand All @@ -240,7 +166,9 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(
process.out.bam,
process.out.versions).match() }
)
}

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