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Swap transdecoder predict to nf-test #7296
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8f70d42
Swap transdecoder predict to nf-test
SPPearce 73a4e1b
Test content rather than md5sum
SPPearce e0103f4
Merge branch 'master' into transdecoder_predict
SPPearce 36bcb12
Merge branch 'master' into transdecoder_predict
SPPearce 4794ec4
Merge branch 'master' into transdecoder_predict
SPPearce 0d8290e
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,4 +2,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - bioconda::transdecoder=5.5.0 | ||
| - bioconda::transdecoder=5.7.1 | ||
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140 changes: 140 additions & 0 deletions
140
modules/nf-core/transdecoder/predict/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process TRANSDECODER_PREDICT" | ||
| script "../main.nf" | ||
| process "TRANSDECODER_PREDICT" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "transdecoder" | ||
| tag "transdecoder/longorf" | ||
| tag "transdecoder/predict" | ||
|
|
||
| test("sarscov2 - uncompressed") { | ||
|
|
||
| setup { | ||
| run("TRANSDECODER_LONGORF") { | ||
| script "../../longorf/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id: 'test'], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = TRANSDECODER_LONGORF.out.folder | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| // orfs are output in a random order; can't be easily sorted either. | ||
| path(process.out.bed[0][1] ).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| path(process.out.cds[0][1] ).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| path(process.out.gff3[0][1]).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| path(process.out.pep[0][1] ).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("sarscov2 - compressed") { | ||
|
|
||
| setup { | ||
| run("TRANSDECODER_LONGORF") { | ||
| script "../../longorf/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id: 'test'], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) | ||
| ] | ||
| input[1] = TRANSDECODER_LONGORF.out.folder | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| // orfs are output in a random order; can't be easily sorted either. | ||
| path(process.out.bed[0][1] ).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| path(process.out.cds[0][1] ).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| path(process.out.gff3[0][1]).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| path(process.out.pep[0][1] ).getText().contains("ID=GENE.MT192765.1~~MT192765.1.p7"), | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("sarscov2 - uncompressed - stub") { | ||
|
|
||
| options "-stub" | ||
|
|
||
| setup { | ||
| run("TRANSDECODER_LONGORF") { | ||
| script "../../longorf/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id: 'test'], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = TRANSDECODER_LONGORF.out.folder | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
123 changes: 123 additions & 0 deletions
123
modules/nf-core/transdecoder/predict/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| { | ||
| "sarscov2 - uncompressed - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.pep:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.cds:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "3": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.bed:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "4": [ | ||
| "versions.yml:md5,d68aca63cf424e1cc9f544b5b3aa9c99" | ||
| ], | ||
| "bed": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.bed:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "cds": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.cds:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "gff3": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "pep": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "genome.fasta.transdecoder.pep:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,d68aca63cf424e1cc9f544b5b3aa9c99" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2025-01-13T19:14:55.271439958" | ||
| }, | ||
| "sarscov2 - uncompressed": { | ||
| "content": [ | ||
| false, | ||
| false, | ||
| true, | ||
| false, | ||
| [ | ||
| "versions.yml:md5,d68aca63cf424e1cc9f544b5b3aa9c99" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2025-01-14T17:04:13.113096174" | ||
| }, | ||
| "sarscov2 - compressed": { | ||
| "content": [ | ||
| false, | ||
| false, | ||
| true, | ||
| false, | ||
| [ | ||
| "versions.yml:md5,d68aca63cf424e1cc9f544b5b3aa9c99" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.2", | ||
| "nextflow": "24.10.3" | ||
| }, | ||
| "timestamp": "2025-01-14T17:00:33.707348893" | ||
| } | ||
| } |
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Your Singularity image is still at version 5.5.0, causing the tests to fail.
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Aah, thanks!