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Added nf-test for gubbins #6598
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
|
|
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| nextflow_process { | ||
|
|
||
| name "Test Process GUBBINS" | ||
| script "../main.nf" | ||
| process "GUBBINS" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "gubbins" | ||
|
|
||
| test("test-gubbins") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) | ||
|
|
||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.fasta, | ||
| process.out.gff, | ||
| path(process.out.vcf[0]).vcf.variantsMD5, | ||
| process.out.stats, | ||
| process.out.phylip, | ||
| file(process.out.embl_predicted[0]).name, // empty | ||
| process.out.embl_branch, | ||
| process.out.tree[0].collect { file(it).name }, // unstable | ||
| file(process.out.tree_labelled[0]).name, // unstable | ||
| process.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("test-gubbins-stub") { | ||
| options '-stub' | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) | ||
|
|
||
| """ | ||
| } | ||
| } | ||
|
|
||
| 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 +1,113 @@ | ||
| { | ||
| "test-gubbins-stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "1": [ | ||
| "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "2": [ | ||
| "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "3": [ | ||
| "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "4": [ | ||
| "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "5": [ | ||
| "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "6": [ | ||
| "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "7": [ | ||
| [ | ||
| "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e", | ||
| "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "8": [ | ||
| "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "9": [ | ||
| "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" | ||
| ], | ||
| "embl_branch": [ | ||
| "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "embl_predicted": [ | ||
| "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "fasta": [ | ||
| "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "gff": [ | ||
| "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "phylip": [ | ||
| "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "stats": [ | ||
| "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "tree": [ | ||
| [ | ||
| "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e", | ||
| "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "tree_labelled": [ | ||
| "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "vcf": [ | ||
| "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-09-06T14:20:39.212181" | ||
| }, | ||
| "test-gubbins": { | ||
| "content": [ | ||
| [ | ||
| "all_sites.filtered_polymorphic_sites.fasta:md5,0f945512f071fd1599bb7455492e31bc" | ||
| ], | ||
| [ | ||
| "all_sites.recombination_predictions.gff:md5,7605a21ad8812866adbdb5cada8a59d4" | ||
| ], | ||
| "d314daa06c635c0b31b132a1092ee4e3", | ||
| [ | ||
| "all_sites.per_branch_statistics.csv:md5,8012a76a2486a8b3dfe78d6902b56ed4" | ||
| ], | ||
| [ | ||
| "all_sites.filtered_polymorphic_sites.phylip:md5,d28da2dd14d08bbb996756064516aee1" | ||
| ], | ||
| "all_sites.recombination_predictions.embl", | ||
| [ | ||
| "all_sites.branch_base_reconstruction.embl:md5,9dfd7e411404360ce4a7938aab8db701" | ||
| ], | ||
| [ | ||
| "all_sites.final_tree.tre", | ||
| "all_sites.node_labelled.final_tree.tre" | ||
| ], | ||
| "all_sites.node_labelled.final_tree.tre", | ||
| [ | ||
| "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-09-06T14:16:35.669362" | ||
| } | ||
| } |
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The test name
test-gubbinsis obvious so, better to have the name of the test contain details of the test-data being used.Thoughts ?
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Good idea. I have updated the names now!