Skip to content

Commit

Permalink
bugfix tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@tillenglert
tillenglert committed Jul 1, 2024
1 parent 2d5d29d commit 19d09ed
Show file tree
Hide file tree
Showing 8 changed files with 21 additions and 29 deletions.
6 changes: 3 additions & 3 deletions tests/pipeline/test_all.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,9 +43,9 @@ nextflow_pipeline {
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },

{ assert snapshot(path("$outputDir/logs/download_proteins.log"),
path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/download_proteins.log").exists() },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() }

{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.1.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.2.tsv.gz").exists() },
Expand Down
1 change: 0 additions & 1 deletion tests/pipeline/test_all.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@
},
"logs": {
"content": [
"download_proteins.log:md5,488e1962cf079d466188481d526495f2",
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"timestamp": "2024-06-26T08:14:54+0000"
Expand Down
14 changes: 7 additions & 7 deletions tests/pipeline/test_mouse.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,17 +23,17 @@ 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("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/db_tables/peptides.tsv.gz").exists() },
{ assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() },
{ assert new File("$outputDir/db_tables/proteins.tsv.gz").exists() },
{ assert new File("$outputDir/db_tables/entities_proteins.tsv").exists() },
{ assert new File("$outputDir/db_tables/microbiomes_entities.no_weights.tsv").exists() },
{ assert new File("$outputDir/db_tables/microbiomes_entities.tsv").exists() },
{ assert new File("$outputDir/db_tables/proteins_peptides.tsv").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() },
Expand All @@ -44,9 +44,9 @@ nextflow_pipeline {
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.H2-Db.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.H2-Db.pdf").exists() },

{ assert snapshot(path("$outputDir/logs/download_proteins.log"),
path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/WARNING_unify_peptide_lengths.log").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/download_proteins.log").exists() },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() }

{ assert new File("$outputDir/prodigal/proteins.pred_1.tsv.gz").exists() }
)
Expand Down
17 changes: 6 additions & 11 deletions tests/pipeline/test_mouse.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,17 +1,13 @@
{
"db_tables": {
"content": [
"alleles.tsv:md5,314847ac5a69fe93ce75c6db0c2496d8",
"conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8",
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
"entities_proteins.tsv:md5,cecff3ce2ac524fdac72635655da6e52",
"entities.tsv:md5,1b26a72cb5f731ba04ed53b6e69237b7",
"microbiomes_entities.no_weights.tsv:md5,55eae24113e41d074d4b2e91912d7be6",
"microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66",
"microbiomes_entities.tsv:md5,2f5498195df08c86eacba2ae76096902",
"microbiomes.tsv:md5,2130005595bdc7ffc770d8304fd9a936",
"proteins_peptides.tsv:md5,bece4df05028af8d221e569755fadb46",
"stats.txt:md5,6e5ecca241fb1cd3fea7ea66c4b81e2a"
"entities.tsv:md5,c766a12bbb1d4ef4707be7077f774191",
"microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832",
"microbiomes.tsv:md5,05bafa72c953e6cb0bd72c296d6fe707",
"stats.txt:md5,c10c27a1ba080ff59dcb5b62467129b2"
],
"timestamp": "2024-06-26T08:14:54+0000"
},
Expand All @@ -23,7 +19,6 @@
},
"logs": {
"content": [
"download_proteins.log:md5,488e1962cf079d466188481d526495f2",
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"timestamp": "2024-06-26T08:14:54+0000"
Expand Down
4 changes: 2 additions & 2 deletions tests/pipeline/test_taxa_only.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,8 @@ nextflow_pipeline {
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },

{ assert snapshot(path("$outputDir/logs/download_proteins.log"),
path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/download_proteins.log").exists() },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() }
)
}
Expand Down
3 changes: 1 addition & 2 deletions tests/pipeline/test_taxa_only.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,13 +13,12 @@
},
"entrez_data": {
"content": [
"microbiomes_entities.entrez.tsv:md5,d74ec125c02485cae58a08a334bf4844",
"microbiomes_entities.entrez.tsv:md5,d74ec125c02485cae58a08a334bf4844"
],
"timestamp": "2024-06-26T08:14:54+0000"
},
"logs": {
"content": [
"download_proteins.log:md5,488e1962cf079d466188481d526495f2",
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"timestamp": "2024-06-26T08:14:54+0000"
Expand Down
4 changes: 2 additions & 2 deletions tests/pipeline/test_taxa_specific_assembly.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,8 @@ nextflow_pipeline {
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },

{ assert snapshot(path("$outputDir/logs/download_proteins.log"),
path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/download_proteins.log").exists() },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() }
)
}
Expand Down
1 change: 0 additions & 1 deletion tests/pipeline/test_taxa_specific_assembly.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
},
"logs": {
"content": [
"download_proteins.log:md5,3541b1a634ac76fc4617d474d7373a78",
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"timestamp": "2024-06-26T08:14:54+0000"
Expand Down

0 comments on commit 19d09ed

Please sign in to comment.