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Added nf-test for vrhyme/vrhyme #6533

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merged 3 commits into from
Sep 3, 2024
Merged

Added nf-test for vrhyme/vrhyme #6533

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334502f
Added nf-test for vrhyme/vrhyme
GallVp Sep 2, 2024
39c751d
Locked dependency versions
GallVp Sep 2, 2024
758f64e
Updated power assertions
GallVp Sep 3, 2024
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4 changes: 3 additions & 1 deletion modules/nf-core/vrhyme/vrhyme/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@ name: vrhyme_vrhyme
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::vrhyme=1.1.0
- conda-forge::python=3.10.8 # Locked with the container
- conda-forge::numpy=1.23.5 # Locked with the container
- conda-forge::scikit-learn=1.2.2 # Locked with the container
2 changes: 1 addition & 1 deletion modules/nf-core/vrhyme/vrhyme/meta.yml
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Expand Up @@ -13,7 +13,7 @@ tools:
documentation: https://github.com/AnantharamanLab/vRhyme
tool_dev_url: https://github.com/AnantharamanLab/vRhyme
doi: 10.1093/nar/gkac341
licence: "['GPL v3', 'GPL v3 license']"
licence: ["GPL v3", "GPL v3 license"]
input:
- meta:
type: map
Expand Down
88 changes: 88 additions & 0 deletions modules/nf-core/vrhyme/vrhyme/tests/main.nf.test
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@@ -0,0 +1,88 @@

nextflow_process {

name "Test Process VRHYME_VRHYME"
script "../main.nf"
process "VRHYME_VRHYME"

tag "modules"
tag "modules_nfcore"
tag "modules_vrhyme"
tag "vrhyme"
tag "vrhyme/vrhyme"
tag "gunzip"

setup {
run("GUNZIP") {
script "../../../gunzip/main.nf"
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
]

"""
}
}
}

test("test-vrhyme-vrhyme") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
]
]
input[1] = GUNZIP.out.gunzip

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.bins[0][1]).listFiles().collect { it.name }.toSorted(), // Some files are unstable
process.out.membership,
file(process.out.summary[0][1]).name, // unstable
process.out.versions
).match()
}
)
}
}

test("test-vrhyme-vrhyme-stub") {
options '-stub'
when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
]
]
input[1] = GUNZIP.out.gunzip

"""
}
}

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

}
169 changes: 169 additions & 0 deletions modules/nf-core/vrhyme/vrhyme/tests/main.nf.test.snap
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@@ -0,0 +1,169 @@
{
"test-vrhyme-vrhyme": {
"content": [
[
"vRhyme_bin_1.faa",
"vRhyme_bin_1.fasta",
"vRhyme_bin_1.ffn",
"vRhyme_bin_10.faa",
"vRhyme_bin_10.fasta",
"vRhyme_bin_10.ffn",
"vRhyme_bin_11.faa",
"vRhyme_bin_11.fasta",
"vRhyme_bin_11.ffn",
"vRhyme_bin_12.faa",
"vRhyme_bin_12.fasta",
"vRhyme_bin_12.ffn",
"vRhyme_bin_13.faa",
"vRhyme_bin_13.fasta",
"vRhyme_bin_13.ffn",
"vRhyme_bin_14.faa",
"vRhyme_bin_14.fasta",
"vRhyme_bin_14.ffn",
"vRhyme_bin_2.faa",
"vRhyme_bin_2.fasta",
"vRhyme_bin_2.ffn",
"vRhyme_bin_3.faa",
"vRhyme_bin_3.fasta",
"vRhyme_bin_3.ffn",
"vRhyme_bin_4.faa",
"vRhyme_bin_4.fasta",
"vRhyme_bin_4.ffn",
"vRhyme_bin_5.faa",
"vRhyme_bin_5.fasta",
"vRhyme_bin_5.ffn",
"vRhyme_bin_6.faa",
"vRhyme_bin_6.fasta",
"vRhyme_bin_6.ffn",
"vRhyme_bin_7.faa",
"vRhyme_bin_7.fasta",
"vRhyme_bin_7.ffn",
"vRhyme_bin_8.faa",
"vRhyme_bin_8.fasta",
"vRhyme_bin_8.ffn",
"vRhyme_bin_9.faa",
"vRhyme_bin_9.fasta",
"vRhyme_bin_9.ffn"
],
[
[
{
"id": "test",
"single_end": false
},
"vRhyme_best_bins.19.membership.tsv:md5,a24fe8417dd21c2db3da84cf51cff750"
]
],
"vRhyme_best_bins.19.summary.tsv",
[
"versions.yml:md5,3806574bd72718ff75e849d015ed0097"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-03T21:20:45.925942"
},
"test-vrhyme-vrhyme-stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
[
"vRhyme_bin_1.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_10.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_11.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_12.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_13.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_14.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_3.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_4.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_5.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_6.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_7.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_8.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_9.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"vRhyme_best_bins.19.membership.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test",
"single_end": false
},
"vRhyme_best_bins.19.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
"versions.yml:md5,3806574bd72718ff75e849d015ed0097"
],
"bins": [
[
{
"id": "test",
"single_end": false
},
[
"vRhyme_bin_1.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_10.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_11.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_12.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_13.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_14.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_3.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_4.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_5.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_6.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_7.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_8.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"vRhyme_bin_9.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"membership": [
[
{
"id": "test",
"single_end": false
},
"vRhyme_best_bins.19.membership.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"summary": [
[
{
"id": "test",
"single_end": false
},
"vRhyme_best_bins.19.summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,3806574bd72718ff75e849d015ed0097"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-02T16:38:33.310046"
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -945,6 +945,3 @@ vrhyme/extractunbinned:
vrhyme/linkbins:
- modules/nf-core/vrhyme/linkbins/**
- tests/modules/nf-core/vrhyme/linkbins/**
vrhyme/vrhyme:
- modules/nf-core/vrhyme/vrhyme/**
- tests/modules/nf-core/vrhyme/vrhyme/**
25 changes: 0 additions & 25 deletions tests/modules/nf-core/vrhyme/vrhyme/main.nf
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5 changes: 0 additions & 5 deletions tests/modules/nf-core/vrhyme/vrhyme/nextflow.config
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63 changes: 0 additions & 63 deletions tests/modules/nf-core/vrhyme/vrhyme/test.yml
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