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port parabricks/indexgvcf to nf-test (#6996)
* port parabricks/indexgvcf to nf-test * fix linting * update test yaml * remove test.yml * remove log * add to conda_skip * add tag gpu * try different profile combination * avoid string concatination * revert changes to profile * update snap - sorry * fix: testfile paths * fix: index file is now created * fix linting * Update modules/nf-core/parabricks/indexgvcf/main.nf --------- Co-authored-by: Matthias Hörtenhuber <[email protected]>
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109 changes: 109 additions & 0 deletions
109
modules/nf-core/parabricks/indexgvcf/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process PARABRICKS_INDEXGVCF" | ||
| script "../main.nf" | ||
| process "PARABRICKS_INDEXGVCF" | ||
|
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "parabricks" | ||
| tag "parabricks/indexgvcf" | ||
| tag "gpu" | ||
|
|
||
| test("human - gvcf") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| file(process.out.gvcf_index[0][1]).name, | ||
| process.out.versions | ||
| ).match() | ||
| } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
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| test("human - gvcf.gz") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
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| test("human - gvcf - stub") { | ||
|
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| options "-stub" | ||
|
|
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| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
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||
| test("human - gvcf.gz - stub") { | ||
|
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| options "-stub" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
114 changes: 114 additions & 0 deletions
114
modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| { | ||
| "human - gvcf.gz": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4" | ||
| ], | ||
| "gvcf_index": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-12-10T10:16:48.994612337" | ||
| }, | ||
| "human - gvcf": { | ||
| "content": [ | ||
| "test.genome.g.vcf.idx", | ||
| [ | ||
| "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-12-10T10:21:20.010561875" | ||
| }, | ||
| "human - gvcf - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4" | ||
| ], | ||
| "gvcf_index": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-12-10T10:21:32.292223281" | ||
| }, | ||
| "human - gvcf.gz - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4" | ||
| ], | ||
| "gvcf_index": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.2" | ||
| }, | ||
| "timestamp": "2024-12-10T10:14:58.744532337" | ||
| } | ||
| } |
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