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Merge branch 'nf-test_assertions' into ci_test_branch_nf-core
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@tillenglert
tillenglert committed Jul 11, 2024
2 parents 52effa3 + e328b1c commit 7573f4a
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Showing 26 changed files with 275 additions and 104 deletions.
2 changes: 1 addition & 1 deletion tests/pipeline/test.nf.test
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Expand Up @@ -31,8 +31,8 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },

{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
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24 changes: 18 additions & 6 deletions tests/pipeline/test.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,33 @@
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8",
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
"entities_proteins.tsv:md5,d008f6c7518e9932de2159751cb2519c",
"entities_proteins.tsv:md5,58bec9a717a9ea802cedf258db60efaa",
"entities.tsv:md5,5aa057079ae45d1e0fd86ebcaa18af0f",
"microbiomes_entities.no_weights.tsv:md5,4d45837586c7c6dc4a19b41735215b01",
"microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66",
"microbiomes_entities.tsv:md5,37690c15b6151ff0622130b8672cddb1",
"microbiomes.tsv:md5,20f141ba0c97325e9d99a9c0765f9a37",
"proteins_peptides.tsv:md5,09f90e7895eca070c9301a4b818fa240",
"stats.txt:md5,83204291158696ce5d19c4e976f38efe"
"proteins_peptides.tsv:md5,58547bc2efb9ae4f154710bb58d14c54",
"peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9",
"proteins.tsv.gz:md5,07964ef2abee962131338b180399a4ee",
"predictions.tsv.gz:md5,c833bdb8d00e719b83e5decd1644c2c9",
"stats.txt:md5,910aff94c66e62a31d28dda6e03b916f"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-10T18:08:31.711958907"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
}
11 changes: 5 additions & 6 deletions tests/pipeline/test_all.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -22,19 +22,18 @@ nextflow_pipeline {
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
path("$outputDir/db_tables/entities_proteins.tsv"),
path("$outputDir/db_tables/entities.tsv"),
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
path("$outputDir/db_tables/microbiomes_entities.tsv"),
path("$outputDir/db_tables/microbiomes.tsv"),
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/entities_proteins.tsv"),
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
path("$outputDir/db_tables/microbiomes_entities.tsv"),
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },

{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },

{ assert snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") },
{ assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() },
{ assert new File("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() },
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42 changes: 31 additions & 11 deletions tests/pipeline/test_all.nf.test.snap
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@@ -1,26 +1,46 @@
{
"entrez_data": {
"content": [
"microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
},
"db_tables": {
"content": [
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,0e992c19471bb56c9b6e6a6f71302742",
"conditions.tsv:md5,87707cd0dee14b0ca4face090ba9dce9",
"entities_proteins.tsv:md5,dfb070f991b705ad1d85dd48dcd5dd0c",
"entities.tsv:md5,8ae4f7ebc592712f45dea1ceaf5a18c0",
"microbiomes_entities.no_weights.tsv:md5,19a44189e6977fc64b78198ad609507a",
"microbiomes_entities.nucl.tsv:md5,aa0d4cc3546508c8e5b81bc9b4b16e39",
"microbiomes_entities.tsv:md5,78b8a81a3abca87ddca748efd14c64ec",
"microbiomes.tsv:md5,70871c8b3023f5a8412c05f4a69dda2f",
"stats.txt:md5,896155e0f043f30bd71c38c8ee7b466c"
],
"timestamp": "2024-06-26T08:14:54+0000"
},
"entrez_data": {
"content": [
"microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072"
"proteins_peptides.tsv:md5,1c0a8c8ea8fbd85d0576714b5220b411",
"peptides.tsv.gz:md5,36aba6d50b1aad95859a547b06d04fc5",
"proteins.tsv.gz:md5,b8c74032604f6ef5c3d73fdf8950aa6b",
"predictions.tsv.gz:md5,96d585b8d153fa93681c80f1bf02290f",
"stats.txt:md5,b04463d0268b44814c2a1170a28b1a86"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-10T19:59:33.708954186"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-10T11:53:04.064515848"
}
}
}
2 changes: 1 addition & 1 deletion tests/pipeline/test_assembly_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },

{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
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22 changes: 17 additions & 5 deletions tests/pipeline/test_assembly_only.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,33 @@
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
"entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6",
"entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6",
"entities.tsv:md5,52312b19a8f3e5c4412afa130179c145",
"microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19",
"microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7",
"microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e",
"microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128",
"proteins_peptides.tsv:md5,fea5ec6926a79d562fe7995db16b4af0",
"proteins_peptides.tsv:md5,ff31eacf91875205291a83f742350318",
"peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b",
"proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de",
"predictions.tsv.gz:md5,e34159d38c4fb47abb02e2ad250ff138",
"stats.txt:md5,d138e30d814db5203a789b7eddd04732"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-10T18:11:18.888885337"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
}
2 changes: 1 addition & 1 deletion tests/pipeline/test_bins_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },

{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
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24 changes: 18 additions & 6 deletions tests/pipeline/test_bins_only.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,33 @@
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
"conditions.tsv:md5,5b04349198a406fc16760c7e8808bb23",
"entities_proteins.tsv:md5,20e495ff06ccacb0f81dbd65e556fc83",
"entities_proteins.tsv:md5,9701a83abaf10c00ff5d7dc002b01a1c",
"entities.tsv:md5,7a472316b8e96e9b12d7ca3ff6a88d39",
"microbiomes_entities.no_weights.tsv:md5,bf3ff9d0390b49c6ecafd89c93909b67",
"microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832",
"microbiomes_entities.tsv:md5,2f40573eb52f3d823aad2f09a639eee2",
"microbiomes.tsv:md5,3f58c3029d21a59316861c28af4361d1",
"proteins_peptides.tsv:md5,4a41affbbc888802cf9202ec1c2ab8a4",
"stats.txt:md5,62d598a845aff61f2be843daa250f485"
"proteins_peptides.tsv:md5,d93e37f0160156298abbb5106ac10aa5",
"peptides.tsv.gz:md5,34497a1a57af3c3e48fceb762cf94f75",
"proteins.tsv.gz:md5,e3c66cf6c5a54a52478a104f23d0d606",
"predictions.tsv.gz:md5,4699fcd56d1af1dd7f9ed7dd41b7ae64",
"stats.txt:md5,a5ef37919a11263ff387e859d1e8c33c"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-10T18:48:27.027414679"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
}
2 changes: 1 addition & 1 deletion tests/pipeline/test_coassembly.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },

{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
Expand Down
24 changes: 18 additions & 6 deletions tests/pipeline/test_coassembly.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,33 @@
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,ad6438cc0e62033f39629d7d002169b5",
"conditions.tsv:md5,092aba068d94feb11b61a22d694359d7",
"entities_proteins.tsv:md5,59e2e25ec73cbdf908d474d4abba6716",
"entities_proteins.tsv:md5,1e64633559bc88f0ce96550d821a2f73",
"entities.tsv:md5,e11b4c3cae16172e0643416fe1e55e0e",
"microbiomes_entities.no_weights.tsv:md5,45512c04e01b2f652b60c5438377411e",
"microbiomes_entities.nucl.tsv:md5,2f884256b54995a265af83b2eb68e773",
"microbiomes_entities.tsv:md5,212fd9b2d8fd3340beac070b812f88e9",
"microbiomes.tsv:md5,b89503022fcbd9b7d7f9eefe7cbccf0f",
"proteins_peptides.tsv:md5,39bc2a204d8bfb5f01c99451ede47c34",
"stats.txt:md5,f2957aced6994532212f0d25b3efba98"
"proteins_peptides.tsv:md5,58547bc2efb9ae4f154710bb58d14c54",
"peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9",
"proteins.tsv.gz:md5,2d25ff5eb066f3ddc8aa71a7acf5f3ce",
"predictions.tsv.gz:md5,998fcc2d79f0c9e340dd678187d12635",
"stats.txt:md5,027c733d48c47409486c8c1b4425bb7a"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-10T19:22:30.912008946"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
}
2 changes: 1 addition & 1 deletion tests/pipeline/test_mhcflurry.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },

{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
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19 changes: 15 additions & 4 deletions tests/pipeline/test_mhcflurry.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,32 @@
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
"entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6",
"entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6",
"entities.tsv:md5,52312b19a8f3e5c4412afa130179c145",
"microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19",
"microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7",
"microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e",
"microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128",
"proteins_peptides.tsv:md5,fea5ec6926a79d562fe7995db16b4af0",
"proteins_peptides.tsv:md5,ff31eacf91875205291a83f742350318",
"peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b",
"proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de",
"predictions.tsv.gz:md5,0df02a33f17a057f5da6775a21f73056",
"stats.txt:md5,d138e30d814db5203a789b7eddd04732"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-11T08:25:27.152248406"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d2bb11e8da2c2003b18054bb1e6843ca"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
}
2 changes: 1 addition & 1 deletion tests/pipeline/test_mhcnuggets_1.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },

{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
Expand Down
19 changes: 15 additions & 4 deletions tests/pipeline/test_mhcnuggets_1.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,32 @@
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
"entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6",
"entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6",
"entities.tsv:md5,52312b19a8f3e5c4412afa130179c145",
"microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19",
"microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7",
"microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e",
"microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128",
"proteins_peptides.tsv:md5,fea5ec6926a79d562fe7995db16b4af0",
"proteins_peptides.tsv:md5,ff31eacf91875205291a83f742350318",
"peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b",
"proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de",
"predictions.tsv.gz:md5,d6672533fdd7ed61cac6e420a0fccb90",
"stats.txt:md5,d138e30d814db5203a789b7eddd04732"
],
"timestamp": "2024-06-26T08:14:54+0000"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-11T08:27:02.891779522"
},
"logs": {
"content": [
"prediction_warnings.log:md5,7c11afacf5a3060459cf58d3bd032230"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
}
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