Added nf-test for somalier/ancestry #7380
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| nextflow_process { | ||||||||
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| name "Test Process SOMALIER_ANCESTRY" | ||||||||
| config "./nextflow.test.config" | ||||||||
| script "../main.nf" | ||||||||
| process "SOMALIER_ANCESTRY" | ||||||||
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| tag "modules" | ||||||||
| tag "modules_nfcore" | ||||||||
| tag "somalier" | ||||||||
| tag "somalier/extract" | ||||||||
| tag "somalier/ancestry" | ||||||||
| tag "untar" | ||||||||
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| setup { | ||||||||
| run("UNTAR") { | ||||||||
| script "../../../untar/main.nf" | ||||||||
| params { | ||||||||
| module_args = "--wildcards '*.somalier'" | ||||||||
| } | ||||||||
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| process { | ||||||||
| """ | ||||||||
| labelled_somalier_tar = file("https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz") | ||||||||
| input[0] = [[id:"1kg"],labelled_somalier_tar] | ||||||||
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| """ | ||||||||
| } | ||||||||
| } | ||||||||
| } | ||||||||
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| test("test_somalier_ancestry") { | ||||||||
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| when { | ||||||||
| params { | ||||||||
| module_args = '' | ||||||||
| } | ||||||||
| process { | ||||||||
| """ | ||||||||
| whole_genome_sommalier = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/whole_genome.somalier", checkIfExists: true) | ||||||||
| labels = file("https://github.com/brentp/somalier/raw/73db124d3fe9febe3a53787707554f863595b48f/scripts/ancestry-labels-1kg.tsv", checkIfExists: true) | ||||||||
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There was a problem hiding this comment. these probably need to be moved from delete_me and also both to the test_datasets repo |
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| ch_labels = Channel.of([[id:"1kg"], labels]) | ||||||||
| ch_whole_genome_somalier = Channel.of([[id:"test"], whole_genome_sommalier]) | ||||||||
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| input[0] = Channel.of([[id:"test"],whole_genome_sommalier]) | ||||||||
| input[1] = ch_labels.join(UNTAR.out.untar) | ||||||||
| """ | ||||||||
| } | ||||||||
| } | ||||||||
| then { | ||||||||
| assertAll( | ||||||||
| { assert process.success }, | ||||||||
| { assert snapshot( | ||||||||
| path(process.out.tsv[0][1]).text.contains('AFR AFR'), | ||||||||
| path(process.out.html[0][1]).text.contains('"ancestry_label":"AMR"'), | ||||||||
| process.out.versions | ||||||||
| ).match() | ||||||||
| } | ||||||||
| ) | ||||||||
| } | ||||||||
| } | ||||||||
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| test("test_somalier_ancestry -- stub") { | ||||||||
| options '-stub' | ||||||||
| when { | ||||||||
| params { | ||||||||
| module_args = '' | ||||||||
| } | ||||||||
| process { | ||||||||
| """ | ||||||||
| whole_genome_sommalier = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/somalier/whole_genome.somalier", checkIfExists: true) | ||||||||
| labels = file("https://github.com/brentp/somalier/raw/73db124d3fe9febe3a53787707554f863595b48f/scripts/ancestry-labels-1kg.tsv", checkIfExists: true) | ||||||||
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| ch_labels = Channel.of([[id:"1kg"], labels]) | ||||||||
| ch_whole_genome_somalier = Channel.of([[id:"test"], whole_genome_sommalier]) | ||||||||
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| input[0] = Channel.of([[id:"test"],whole_genome_sommalier]) | ||||||||
| input[1] = ch_labels.join(UNTAR.out.untar) | ||||||||
| """ | ||||||||
| } | ||||||||
| } | ||||||||
| then { | ||||||||
| assertAll( | ||||||||
| { assert process.success }, | ||||||||
| { assert snapshot(process.out).match() } | ||||||||
| ) | ||||||||
| } | ||||||||
| } | ||||||||
| } | ||||||||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| { | ||
| "test_somalier_ancestry": { | ||
| "content": [ | ||
| true, | ||
| true, | ||
| [ | ||
| "versions.yml:md5,75c0cd29fd1bf99528a819954cff93c6" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2025-01-28T09:39:02.833629" | ||
| }, | ||
| "test_somalier_ancestry -- stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "somalier-ancestry.somalier-ancestry.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "somalier-ancestry.somalier-ancestry.html:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| "versions.yml:md5,75c0cd29fd1bf99528a819954cff93c6" | ||
| ], | ||
| "html": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "somalier-ancestry.somalier-ancestry.html:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "tsv": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "somalier-ancestry.somalier-ancestry.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,75c0cd29fd1bf99528a819954cff93c6" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2025-01-28T09:41:31.001304" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| process { | ||
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| withName: "UNTAR" { | ||
| ext.args2 = params.module_args | ||
| } | ||
| } |
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removed because it cannot be used?