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Fix nf-tests #463

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Merged
jasmezz merged 1 commit into from
Mar 4, 2025
Merged

Fix nf-tests #463

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1 change: 0 additions & 1 deletion tests/test.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,6 @@ nextflow_pipeline {
{ assert snapshot(
path("$outputDir/reports/ampcombi2/Ampcombi_cluster.log"),
path("$outputDir/reports/ampcombi2/Ampcombi_complete.log"),
path("$outputDir/reports/ampcombi2/Ampcombi_parse_tables.log")
).match("ampcombi_logfiles") },

// DeepARG
Expand Down
3 changes: 1 addition & 2 deletions tests/test.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,7 @@
"ampcombi_logfiles": {
"content": [
"Ampcombi_cluster.log:md5,4c78f5f134edf566f39e04e3ab7d8558",
"Ampcombi_complete.log:md5,3dabfea4303bf94bd4f5d78c5b8c83c1",
"Ampcombi_parse_tables.log:md5,ff27d0c3657ce99d2c29a136f598e4f8"
"Ampcombi_complete.log:md5,3dabfea4303bf94bd4f5d78c5b8c83c1"
],
"meta": {
"nf-test": "0.9.0",
Expand Down
20 changes: 9 additions & 11 deletions tests/test_preannotated.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,6 @@ nextflow_pipeline {
path("$outputDir/amp/macrel/sample_2.macrel/sample_2.macrel.smorfs.faa.gz"),
path("$outputDir/amp/macrel/sample_3.macrel/sample_3.macrel.smorfs.faa.gz"),
path("$outputDir/amp/macrel/sample_1.macrel/sample_1.macrel.all_orfs.faa.gz"),
path("$outputDir/amp/macrel/sample_2.macrel/sample_2.macrel.all_orfs.faa.gz"),
path("$outputDir/amp/macrel/sample_3.macrel/sample_3.macrel.all_orfs.faa.gz"),
path("$outputDir/amp/macrel/sample_1.macrel/sample_1.macrel.prediction.gz"),
path("$outputDir/amp/macrel/sample_2.macrel/sample_2.macrel.prediction.gz"),
Expand All @@ -60,6 +59,8 @@ nextflow_pipeline {
path("$outputDir/amp/macrel/sample_2.macrel/sample_2.macrel_log.txt"),
path("$outputDir/amp/macrel/sample_3.macrel/sample_3.macrel_log.txt")
).match("macrel") },
{ assert new File("$outputDir/amp/macrel/sample_2.macrel/sample_2.macrel.all_orfs.faa.gz").exists() },


// AMPcombi
{ assert snapshot(
Expand Down Expand Up @@ -107,21 +108,18 @@ nextflow_pipeline {
).match("rgi") },

// fARGene
{ assert snapshot(
path("$outputDir/arg/fargene/sample_1/class_a/results_summary.txt"),
path("$outputDir/arg/fargene/sample_2/class_a/results_summary.txt"),
path("$outputDir/arg/fargene/sample_3/class_a/results_summary.txt"),
path("$outputDir/arg/fargene/sample_1/class_b_1_2/results_summary.txt"),
path("$outputDir/arg/fargene/sample_2/class_b_1_2/results_summary.txt"),
path("$outputDir/arg/fargene/sample_3/class_b_1_2/results_summary.txt")
).match("fargene")
},
{ assert path("$outputDir/arg/fargene/sample_1/class_a/results_summary.txt").text.contains("class_A.hmm") },
{ assert path("$outputDir/arg/fargene/sample_2/class_a/results_summary.txt").text.contains("class_A.hmm") },
{ assert path("$outputDir/arg/fargene/sample_3/class_a/results_summary.txt").text.contains("class_A.hmm") },
{ assert path("$outputDir/arg/fargene/sample_1/class_b_1_2/results_summary.txt").text.contains("class_B_1_2.hmm") },
{ assert path("$outputDir/arg/fargene/sample_2/class_b_1_2/results_summary.txt").text.contains("class_B_1_2.hmm") },
{ assert path("$outputDir/arg/fargene/sample_3/class_b_1_2/results_summary.txt").text.contains("class_B_1_2.hmm") },
{ assert path("$outputDir/arg/fargene/sample_1/fargene_analysis.log").text.contains("fARGene is done.") },
{ assert path("$outputDir/arg/fargene/sample_2/fargene_analysis.log").text.contains("fARGene is done.") },
{ assert path("$outputDir/arg/fargene/sample_3/fargene_analysis.log").text.contains("fARGene is done.") },

// hAMRonization
{ assert snapshot(path("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv").readLines().size()).match("hamronization") },
{ assert new File("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv").exists() },

// argNorm
{ assert snapshot(
Expand Down
112 changes: 43 additions & 69 deletions tests/test_preannotated.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,28 @@
{
"abricate": {
"content": [
"sample_1.txt:md5,427cec26e354ac6b0ab6047ec6621202",
"sample_2.txt:md5,4c140c932a48a22bcd8ae911bda8f4c7",
"sample_3.txt:md5,d6534efe3d03173749d003bf9e624e68"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-04T13:44:42.292890292"
},
"rgi": {
"content": [
"sample_1.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955",
"sample_2.txt:md5,cc4ae1fb9e0d5f79ef5105d640c7b748",
"sample_3.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-04T13:44:42.337377281"
},
"deeparg": {
"content": [
"sample_1.align.daa.tsv:md5,0e71c37318bdc6cba792196d0455293d",
Expand Down Expand Up @@ -53,6 +77,19 @@
},
"timestamp": "2024-07-27T08:23:32.486921338"
},
"ampcombi": {
"content": [
"Ampcombi_cluster.log:md5,4c78f5f134edf566f39e04e3ab7d8558",
"Ampcombi_complete.log:md5,3dabfea4303bf94bd4f5d78c5b8c83c1",
true,
true
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-03-04T13:44:42.24263737"
},
"amplify": {
"content": [
true,
Expand Down Expand Up @@ -86,7 +123,6 @@
"sample_2.macrel.smorfs.faa.gz:md5,83ae7b9808d7183d87b41c10253c9c9e",
"sample_3.macrel.smorfs.faa.gz:md5,a4f853b560c6a8c215e0d243c24ec056",
"sample_1.macrel.all_orfs.faa.gz:md5,d1ae1cadc3770994b2ed4982aadd5406",
"sample_2.macrel.all_orfs.faa.gz:md5,d9612a4275a912cabdae13b1ccc1857e",
"sample_3.macrel.all_orfs.faa.gz:md5,d1ae1cadc3770994b2ed4982aadd5406",
"sample_1.macrel.prediction.gz:md5,62146cf9f759c9c6c2c2f9e5ba816119",
"sample_2.macrel.prediction.gz:md5,1b479d31bb7dbf636a2028ddef72f5cc",
Expand All @@ -99,72 +135,10 @@
"sample_3.macrel_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-18T11:50:30.926088397"
},
"hamronization": {
"content": [
246
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-09-05T10:17:06.711064611"
},
"abricate": {
"content": [
"sample_1.txt:md5,427cec26e354ac6b0ab6047ec6621202",
"sample_2.txt:md5,4c140c932a48a22bcd8ae911bda8f4c7",
"sample_3.txt:md5,d6534efe3d03173749d003bf9e624e68"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:24.87794287"
},
"fargene": {
"content": [
"results_summary.txt:md5,2c8a073d2a7938e8aedcc097e6df2aa5",
"results_summary.txt:md5,3b86a5513e89e22a4c8b9279678ce0c0",
"results_summary.txt:md5,2c8a073d2a7938e8aedcc097e6df2aa5",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:25.248986515"
},
"rgi": {
"content": [
"sample_1.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955",
"sample_2.txt:md5,cc4ae1fb9e0d5f79ef5105d640c7b748",
"sample_3.txt:md5,ff8f179d06d8566d8cf779fc7d1f4955"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:25.117843821"
},
"ampcombi": {
"content": [
"Ampcombi_cluster.log:md5,4c78f5f134edf566f39e04e3ab7d8558",
"Ampcombi_complete.log:md5,3dabfea4303bf94bd4f5d78c5b8c83c1",
true,
true
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-07-27T08:11:24.639509225"
"timestamp": "2025-03-04T13:44:42.200904946"
},
"amrfinderplus": {
"content": [
Expand All @@ -173,9 +147,9 @@
"sample_3.tsv:md5,29cfb6f34f420d802eda95c6d9daa361"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-07-27T08:11:24.994284774"
"timestamp": "2025-03-04T13:44:42.316250647"
}
}
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