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added snapshot for all workflows
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added two test cases
    missing phenotypes should cause pipeline failing and no output file
    specify one phenotype should output only one output file
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@AmstlerStephan
AmstlerStephan committed Dec 15, 2023
1 parent 3f5b554 commit c733b9d
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Showing 2 changed files with 98 additions and 83 deletions.
110 changes: 74 additions & 36 deletions tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,42 +38,6 @@ nextflow_pipeline {
assert snapshot(new File("$outputDir/results/Y1.regenie.gz"), new File("$outputDir/results/Y2.regenie.gz") , workflow.trace).match()
}

}

test("Should fail since no phenotype is specified") {

when {

params {
project = 'test-gene-based-test'
genotypes_build = 'hg19'
genotypes_prediction = "$projectDir/tests/input/pipeline/example.{bim,bed,fam}"
genotypes_association = "$projectDir/tests/input/pipeline/example.{bim,bed,fam}"
genotypes_association_format = 'bed'
phenotypes_filename = "$projectDir/tests/input/pipeline/phenotype_bin.txt"
phenotypes_binary_trait = true
phenotypes_columns = ''
covariates_filename = "$projectDir/tests/input/pipeline/covariates.txt"
covariates_columns = 'V1,V2,V3'
regenie_run_gene_based_tests = true
regenie_gene_anno = "$projectDir/tests/input/gene_based_tests/example.annotation"
regenie_gene_setlist = "$projectDir/tests/input/gene_based_tests/example.setlist"
regenie_gene_masks = "$projectDir/tests/input/gene_based_tests/example.masks"
regenie_gene_test = 'skat'
regenie_gene_aaf = 0.01
regenie_gene_vc_max_aaf = 100
regenie_gene_vc_mac_thr = 10
regenie_gene_build_mask = 'sum'
rsids_filename = "$projectDir/tests/input/pipeline/rsids.tsv.gz"
outdir = "$outputDir"
}
}

then {
assert workflow.fail
assert workflow.out.my_channel.size() == 0
}

}

test("Should execute gene-based test pipeline") {
Expand Down Expand Up @@ -901,4 +865,78 @@ test("Should GWAS with chunking and optional step 1 param") {
}


test("Should execute gene-based-test with only one output file") {

when {

params {
project = 'test-gene-based-test'
genotypes_build = 'hg19'
genotypes_prediction = "$projectDir/tests/input/pipeline/example.{bim,bed,fam}"
genotypes_association = "$projectDir/tests/input/pipeline/example.{bim,bed,fam}"
genotypes_association_format = 'bed'
phenotypes_filename = "$projectDir/tests/input/pipeline/phenotype_bin.txt"
phenotypes_binary_trait = true
phenotypes_columns = 'Y1'
covariates_filename = "$projectDir/tests/input/pipeline/covariates.txt"
covariates_columns = 'V1,V2,V3'
regenie_run_gene_based_tests = true
regenie_gene_anno = "$projectDir/tests/input/gene_based_tests/example.annotation"
regenie_gene_setlist = "$projectDir/tests/input/gene_based_tests/example.setlist"
regenie_gene_masks = "$projectDir/tests/input/gene_based_tests/example.masks"
regenie_gene_test = 'skat'
regenie_gene_aaf = 0.01
regenie_gene_vc_max_aaf = 100
regenie_gene_vc_mac_thr = 10
regenie_gene_build_mask = 'sum'
rsids_filename = "$projectDir/tests/input/pipeline/rsids.tsv.gz"
outdir = "$outputDir"
}
}

then {
assert workflow.success
snapshot(new File("$outputDir/results/Y1.regenie.gz"), workflow.trace).match()
}

}


test("Should fail since no phenotype is specified") {

when {

params {
project = 'test-gene-based-test'
genotypes_build = 'hg19'
genotypes_prediction = "$projectDir/tests/input/pipeline/example.{bim,bed,fam}"
genotypes_association = "$projectDir/tests/input/pipeline/example.{bim,bed,fam}"
genotypes_association_format = 'bed'
phenotypes_filename = "$projectDir/tests/input/pipeline/phenotype_bin.txt"
phenotypes_binary_trait = true
phenotypes_columns = ''
covariates_filename = "$projectDir/tests/input/pipeline/covariates.txt"
covariates_columns = 'V1,V2,V3'
regenie_run_gene_based_tests = true
regenie_gene_anno = "$projectDir/tests/input/gene_based_tests/example.annotation"
regenie_gene_setlist = "$projectDir/tests/input/gene_based_tests/example.setlist"
regenie_gene_masks = "$projectDir/tests/input/gene_based_tests/example.masks"
regenie_gene_test = 'skat'
regenie_gene_aaf = 0.01
regenie_gene_vc_max_aaf = 100
regenie_gene_vc_mac_thr = 10
regenie_gene_build_mask = 'sum'
rsids_filename = "$projectDir/tests/input/pipeline/rsids.tsv.gz"
outdir = "$outputDir"
}
}

then {
assert workflow.failed
snapshot(workflow.trace).match()
}

}


}
71 changes: 24 additions & 47 deletions tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -169,59 +169,15 @@
},
"Should execute GWAS with header in phenotype file (custom batch size)": {
"content": [
{
"directory": false,
"file": false,
"freeSpace": 0,
"canonicalPath": "/home/nanopore/genepi_hackathon/nf-test/nf-gwas-1/.nf-test/tests/60a3cad7bcdf791d727b26515b05aeb1/output/results/Y1.regenie.gz",
"usableSpace": 0,
"hidden": false,
"totalSpace": 0,
"path": "/home/nanopore/genepi_hackathon/nf-test/nf-gwas-1/.nf-test/tests/60a3cad7bcdf791d727b26515b05aeb1/output/results/Y1.regenie.gz",
"name": "Y1.regenie.gz",
"absolute": true,
"absolutePath": "/home/nanopore/genepi_hackathon/nf-test/nf-gwas-1/.nf-test/tests/60a3cad7bcdf791d727b26515b05aeb1/output/results/Y1.regenie.gz",
"parent": [
"PHENO1.regenie.gz:md5,c03c47e1d4300277f2a445afc14c6d1e",
"PHENO1.regenie.gz.tbi:md5,52c43bd02a8ceff6c362d0b56ff5fbfe",
"PHENO2.regenie.gz:md5,3b600580a44b792462720d7e7c734ccc",
"PHENO2.regenie.gz.tbi:md5,72f72954151e910c9ed849b95ac9b402",
[
"PHENO1.regenie.filtered.gz:md5,1da6cac933d2aa0b38613b96e9a5c517",
"PHENO2.regenie.filtered.gz:md5,8dba8315f5bd13f8ae62c9ba1a7dfce6"
]
]
},
{
"directory": false,
"file": false,
"freeSpace": 0,
"canonicalPath": "/home/nanopore/genepi_hackathon/nf-test/nf-gwas-1/.nf-test/tests/60a3cad7bcdf791d727b26515b05aeb1/output/results/Y2.regenie.gz",
"usableSpace": 0,
"hidden": false,
"totalSpace": 0,
"path": "/home/nanopore/genepi_hackathon/nf-test/nf-gwas-1/.nf-test/tests/60a3cad7bcdf791d727b26515b05aeb1/output/results/Y2.regenie.gz",
"name": "Y2.regenie.gz",
"absolute": true,
"absolutePath": "/home/nanopore/genepi_hackathon/nf-test/nf-gwas-1/.nf-test/tests/60a3cad7bcdf791d727b26515b05aeb1/output/results/Y2.regenie.gz",
"parent": [
"PHENO1.regenie.gz:md5,c03c47e1d4300277f2a445afc14c6d1e",
"PHENO1.regenie.gz.tbi:md5,52c43bd02a8ceff6c362d0b56ff5fbfe",
"PHENO2.regenie.gz:md5,3b600580a44b792462720d7e7c734ccc",
"PHENO2.regenie.gz.tbi:md5,72f72954151e910c9ed849b95ac9b402",
[
"PHENO1.regenie.filtered.gz:md5,1da6cac933d2aa0b38613b96e9a5c517",
"PHENO2.regenie.filtered.gz:md5,8dba8315f5bd13f8ae62c9ba1a7dfce6"
]
]
},
"PHENO1.regenie.gz:md5,c03c47e1d4300277f2a445afc14c6d1e",
"PHENO2.regenie.gz:md5,3b600580a44b792462720d7e7c734ccc",
{
"tasksFailed": 0,
"tasksCount": 40,
"tasksSucceeded": 40
}
],
"timestamp": "2023-12-14T16:44:21.551356"
"timestamp": "2023-12-15T09:39:33.247657"
},
"Should execute GWAS with recessive test": {
"content": [
Expand Down Expand Up @@ -366,6 +322,16 @@
],
"timestamp": "2023-12-14T16:42:19.084491"
},
"Should fail since no phenotype is specified": {
"content": [
{
"tasksFailed": 0,
"tasksCount": 0,
"tasksSucceeded": 0
}
],
"timestamp": "2023-12-15T09:46:31.396474"
},
"Should execute liftover and GWAS pipeline with array results": {
"content": [
"Y1.regenie.gz:md5,2819b6b773587f7f88028281a29bd1a4",
Expand All @@ -378,6 +344,17 @@
],
"timestamp": "2023-12-14T16:39:34.107772"
},
"Should execute gene-based-test with only one output file": {
"content": [
"Y1.regenie.gz:md5,61a5f115619d3ee3c14a34a63e1fe73b",
{
"tasksFailed": 0,
"tasksCount": 9,
"tasksSucceeded": 9
}
],
"timestamp": "2023-12-15T09:53:01.767545"
},
"Should execute GWAS with deletion of missing phenotype data": {
"content": [
"Y1.regenie.gz:md5,3b46e913e302d59a27c87f989384a689",
Expand Down

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