Add stub block and migrate plasmidid to topic channels #11438
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,3 @@ | ||
| nextflow_process { | ||
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| name "Test Process PLASMIDID" | ||
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@@ -27,18 +26,29 @@ nextflow_process { | |
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(sanitizeOutput(process.out, unstableKeys:["images", "logs", "data", "database", "kmer"])).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
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| test("test-plasmidid-stub") { | ||
| options "-stub" | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ [ id:'test' ], // meta map | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) | ||
| ] | ||
| input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
|
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|
Contributor
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||
| """ | ||
| } | ||
| } | ||
|
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||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(sanitizeOutput(process.out, unstableKeys:["images", "logs", "data", "database", "kmer"])).match() } | ||
|
Contributor
There was a problem hiding this comment. In the stub test all the files should be stable. |
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| ) | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,170 @@ | ||
| { | ||
| "test-plasmidid": { | ||
| "content": [ | ||
| { | ||
| "data": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "data" | ||
| ] | ||
| ], | ||
| "database": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "database" | ||
| ] | ||
| ], | ||
| "fasta_files": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| [ | ||
| "MT192765.1_term.fasta:md5,8a8537dd3b21e6905f9367b51c3b3074" | ||
| ] | ||
| ] | ||
| ], | ||
| "html": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test_final_results.html:md5,415774b2cff3a50e4304c875cf72529d" | ||
| ] | ||
| ], | ||
| "images": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "images" | ||
| ] | ||
| ], | ||
| "kmer": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "kmer" | ||
| ] | ||
| ], | ||
| "logs": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "logs" | ||
| ] | ||
| ], | ||
| "tab": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test_final_results.tab:md5,e7e6be8e76cac944979bb3dfc21da8bd" | ||
| ] | ||
| ], | ||
| "versions_plasmidid": [ | ||
| [ | ||
| "PLASMIDID", | ||
| "plasmidid", | ||
| "1.6.4" | ||
| ] | ||
| ] | ||
| } | ||
| ], | ||
| "timestamp": "2026-04-30T12:54:16.108858", | ||
| "meta": { | ||
| "nf-test": "0.9.5", | ||
| "nextflow": "26.04.0" | ||
| } | ||
| }, | ||
| "test-plasmidid-stub": { | ||
| "content": [ | ||
| { | ||
| "data": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "data" | ||
| ] | ||
| ], | ||
| "database": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "database" | ||
| ] | ||
| ], | ||
| "fasta_files": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| [ | ||
|
|
||
| ] | ||
| ] | ||
| ], | ||
| "html": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test_final_results.html:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "images": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "images" | ||
| ] | ||
| ], | ||
| "kmer": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "kmer" | ||
| ] | ||
| ], | ||
| "logs": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "logs" | ||
| ] | ||
| ], | ||
| "tab": [ | ||
| [ | ||
| { | ||
| "id": "test" | ||
| }, | ||
| "test_final_results.tab:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "versions_plasmidid": [ | ||
| [ | ||
| "PLASMIDID", | ||
| "plasmidid", | ||
| "1.6.4" | ||
| ] | ||
| ] | ||
| } | ||
| ], | ||
| "timestamp": "2026-04-30T15:08:17.915883", | ||
| "meta": { | ||
| "nf-test": "0.9.5", | ||
| "nextflow": "26.04.0" | ||
| } | ||
| } | ||
| } |
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This can be simplified as