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Enhancement/adding unit testing #128

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Enhancement/adding unit testing #128

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a1e0987
Updated .gitignore file for testing purposes
rhassaine Jan 29, 2025
cce8831
Generated basic test cases for AMBER process in both tumor/normal & t…
rhassaine Jan 29, 2025
8bf800e
Removed additional logging from test
rhassaine Jan 29, 2025
40df527
Latest AMBER test cases with updated nf-test pckg
rhassaine Jan 31, 2025
c9a16b1
Removed comments
rhassaine Jan 31, 2025
cb2a0f5
Unit testing for COBALT
rhassaine Jan 31, 2025
8552a82
Added unit tests for AMBER (tumor + normal mode) & COBALT
rhassaine Feb 3, 2025
a8d5e94
Additional tests for tumor-only mode
rhassaine Feb 4, 2025
31b1f1c
Indentation fix
rhassaine Feb 4, 2025
bd84a86
Updated .gitignore
rhassaine Feb 4, 2025
621b616
Updated .gitignore w/ test-related files & dirs
rhassaine Feb 4, 2025
fcb9c57
Formatting issues
rhassaine Feb 4, 2025
e3410f0
Added unit testing for sage somatic
rhassaine Feb 4, 2025
6df1caf
Adding ISOFOX testing
rhassaine Feb 5, 2025
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,5 @@ results/
testing/
testing*
*.pyc
null/
.nf-test*
.nf-test/
9 changes: 9 additions & 0 deletions nf-test.config
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config {

testsDir "tests"
workDir ".nf-test"
configFile "tests/nextflow.config"
profile "docker"
options "-dump-channels"

}
101 changes: 101 additions & 0 deletions tests/modules/local/amber/main.nf.test
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nextflow_process {

name "Test Process AMBER"
script "modules/local/amber/main.nf"
process "AMBER"

test("AMBER testing tumor + normal") {

when {
params {
test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'
}
process {
"""
// define inputs of the process here. Example:
// input[0] = file("test-file.txt")

input[0] = [
[id: 'test',
tumor_id: 'tumor_test',
normal_id: 'normal_test'
],

file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
file(params.test_sample_data + 'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
file(params.test_sample_data + 'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),

]

input[1] = 38 // ref_genome_version
input[2] = file("https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/reference_data/hmftools/5.34_38--2/dna_pipeline/copy_number/AmberGermlineSites.38.tsv.gz")
input[3] = []
"""
}
}

then {
// stable_name: All files + folders in ${params.outdir}/ with a stable name
// def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
// assert process.success
// assert snapshot(process.out).match()
def amber_output_dir = process.out.amber_dir[0][1]

assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert path(amber_output_dir).resolve("amber.version").exists() },
{ assert path(amber_output_dir).resolve("normal_test.amber.homozygousregion.tsv").exists() },
{ assert path(amber_output_dir).resolve("normal_test.amber.snp.vcf.gz").exists() },
{ assert path(amber_output_dir).resolve("normal_test.amber.snp.vcf.gz.tbi").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.baf.pcf").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.baf.tsv.gz").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.contamination.tsv").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.contamination.vcf.gz").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.contamination.vcf.gz.tbi").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.qc").exists() },
{ assert path(process.out.versions[0]).exists() }
)
}

}

test("AMBER with tumor only") {
when {
params {
// publish_dir_mode = "symlink"
test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'
}
process {
"""
input[0] = [
[id: 'test', tumor_id: 'tumor_test'],
file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
[],
file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
[]
]
input[1] = 38
input[2] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/AmberGermlineSites.38.tsv.gz")
input[3] = []
"""
}
}

then {
def amber_output_dir = process.out.amber_dir[0][1]

assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert path(amber_output_dir).resolve("amber.version").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.baf.pcf").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.baf.tsv.gz").exists() },
{ assert path(amber_output_dir).resolve("tumor_test.amber.qc").exists() },
{ assert path(process.out.versions[0]).exists() }
)
}
}

}
106 changes: 106 additions & 0 deletions tests/modules/local/amber/main.nf.test.snap
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{
"AMBER testing tumor + normal": {
"content": [
{
"0": [
[
{
"id": "test",
"tumor_id": "tumor_test",
"normal_id": "normal_test"
},
[
"amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
"normal_test.amber.homozygousregion.tsv:md5,d21abd62a26119eaf01ea8d1f66b9f05",
"normal_test.amber.snp.vcf.gz:md5,44f59e7c11b3b348f647e0251732acc6",
"normal_test.amber.snp.vcf.gz.tbi:md5,e4caffcadff308826156914dd6b43484",
"tumor_test.amber.baf.pcf:md5,d4015414e9ccf00ab02c818a2a99a939",
"tumor_test.amber.baf.tsv.gz:md5,7c6921d6c7742598b3e8b3f7fe8fea8d",
"tumor_test.amber.contamination.tsv:md5,6fb3d29cc2c879b1db07cc8581a8fb70",
"tumor_test.amber.contamination.vcf.gz:md5,5562d1e335c40ff733bbf751e37e541c",
"tumor_test.amber.contamination.vcf.gz.tbi:md5,a359216fecd8b0a3eada28dc683300a1",
"tumor_test.amber.qc:md5,9c502425aa5e1bf23569e1f60a32dcf1"
]
]
],
"1": [
"versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
],
"amber_dir": [
[
{
"id": "test",
"tumor_id": "tumor_test",
"normal_id": "normal_test"
},
[
"amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
"normal_test.amber.homozygousregion.tsv:md5,d21abd62a26119eaf01ea8d1f66b9f05",
"normal_test.amber.snp.vcf.gz:md5,44f59e7c11b3b348f647e0251732acc6",
"normal_test.amber.snp.vcf.gz.tbi:md5,e4caffcadff308826156914dd6b43484",
"tumor_test.amber.baf.pcf:md5,d4015414e9ccf00ab02c818a2a99a939",
"tumor_test.amber.baf.tsv.gz:md5,7c6921d6c7742598b3e8b3f7fe8fea8d",
"tumor_test.amber.contamination.tsv:md5,6fb3d29cc2c879b1db07cc8581a8fb70",
"tumor_test.amber.contamination.vcf.gz:md5,5562d1e335c40ff733bbf751e37e541c",
"tumor_test.amber.contamination.vcf.gz.tbi:md5,a359216fecd8b0a3eada28dc683300a1",
"tumor_test.amber.qc:md5,9c502425aa5e1bf23569e1f60a32dcf1"
]
]
],
"versions": [
"versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-04T08:41:54.940934927"
},
"AMBER with tumor only": {
"content": [
{
"0": [
[
{
"id": "test",
"tumor_id": "tumor_test"
},
[
"amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
"tumor_test.amber.baf.pcf:md5,5b42f5fac4df8e88a1605943beda9eda",
"tumor_test.amber.baf.tsv.gz:md5,938d30b5bd65598a4efc2b5c01f89ce1",
"tumor_test.amber.qc:md5,9547e68ba672e08d6bd49e1e6f654ee8"
]
]
],
"1": [
"versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
],
"amber_dir": [
[
{
"id": "test",
"tumor_id": "tumor_test"
},
[
"amber.version:md5,94a3ca487cc956f9eadb8de364c27b1d",
"tumor_test.amber.baf.pcf:md5,5b42f5fac4df8e88a1605943beda9eda",
"tumor_test.amber.baf.tsv.gz:md5,938d30b5bd65598a4efc2b5c01f89ce1",
"tumor_test.amber.qc:md5,9547e68ba672e08d6bd49e1e6f654ee8"
]
]
],
"versions": [
"versions.yml:md5,f5846f28a6cd7391cccfc28a96892710"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-04T08:42:14.429643438"
}
}
88 changes: 88 additions & 0 deletions tests/modules/local/cobalt/main.nf.test
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nextflow_process {

name "Test Process COBALT"
script "modules/local/cobalt/main.nf"
process "COBALT"

test("COBALT testing tumor + normal") {

when {
params {
test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'// define parameters here. Example:
}
process {
"""
// define inputs of the process here. Example:
// input[0] = file("test-file.txt")

input[0] = [
[id: 'test',
tumor_id: 'tumor_test',
normal_id: 'normal_test'
],
file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
file(params.test_sample_data + 'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
file(params.test_sample_data + 'subject_a.normal.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
]
input[1] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/GC_profile.1000bp.38.cnp")
input[2] = []
input[3] = []
"""
}
}

then {
def cobalt_output_dir = process.out.cobalt_dir[0][1]
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert path(cobalt_output_dir).resolve("cobalt.version").exists() },
{ assert path(cobalt_output_dir).resolve("tumor_test.cobalt.gc.median.tsv").exists() },
{ assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.pcf").exists() },
{ assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.tsv.gz").exists() },
{ assert path(cobalt_output_dir).resolve("normal_test.cobalt.gc.median.tsv").exists() },
{ assert path(cobalt_output_dir).resolve("normal_test.cobalt.ratio.median.tsv").exists() },
{ assert path(cobalt_output_dir).resolve("normal_test.cobalt.ratio.pcf").exists() },
{ assert path(process.out.versions[0]).exists() }
)
}

}

test("COBALT with tumor only") {
when {
params {
// publish_dir_mode = "symlink"
test_sample_data = 'https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser/sample_data/simulated_reads/wgts/markdups_bam/'
}
process {
"""
input[0] = [
[id: 'test', tumor_id: 'tumor_test'],
file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam', checkIfExists: true),
[],
file(params.test_sample_data + 'subject_a.tumor.dna.bwa-mem2_2.2.1.markdups.bam.bai', checkIfExists: true),
[]
]
input[1] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/GC_profile.1000bp.38.cnp")
input[2] = file("/home/rhassaine/resource_files_oa/38/results/reference_data/1.0.0/20250203_101759/hmf_data_5.34_38--2/dna_pipeline/copy_number/DiploidRegions.38.bed.gz")
input[3] = []
"""
}
}

then {
def cobalt_output_dir = process.out.cobalt_dir[0][1]
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert path(cobalt_output_dir).resolve("cobalt.version").exists() },
{ assert path(cobalt_output_dir).resolve("tumor_test.cobalt.gc.median.tsv").exists() },
{ assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.pcf").exists() },
{ assert path(cobalt_output_dir).resolve("tumor_test.cobalt.ratio.tsv.gz").exists() },
{ assert path(process.out.versions[0]).exists() }
)
}
}
}
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