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Update all tests
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@tillenglert
tillenglert committed Jul 10, 2024
1 parent 9928067 commit c05d655
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Showing 12 changed files with 53 additions and 52 deletions.
8 changes: 4 additions & 4 deletions tests/pipeline/test.nf.test
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Expand Up @@ -29,17 +29,17 @@ nextflow_pipeline {
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/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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },

{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.2.tsv.gz").exists() },
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17 changes: 9 additions & 8 deletions tests/pipeline/test_all.nf.test
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Expand Up @@ -25,14 +25,15 @@ nextflow_pipeline {
path("$outputDir/db_tables/entities.tsv"),
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
path("$outputDir/db_tables/microbiomes.tsv"),
path("$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/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 @@ -43,9 +44,9 @@ 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("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$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() },
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8 changes: 4 additions & 4 deletions tests/pipeline/test_assembly_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,17 +30,17 @@ nextflow_pipeline {
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/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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },

{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
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8 changes: 4 additions & 4 deletions tests/pipeline/test_bins_only.nf.test
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Expand Up @@ -30,17 +30,17 @@ nextflow_pipeline {
path("$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("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },

{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() }
)
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8 changes: 4 additions & 4 deletions tests/pipeline/test_coassembly.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,17 +30,17 @@ nextflow_pipeline {
path("$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("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },

{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.1.tsv.gz").exists() },
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4 changes: 2 additions & 2 deletions tests/pipeline/test_mhcflurry.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,10 @@ nextflow_pipeline {
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/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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
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4 changes: 2 additions & 2 deletions tests/pipeline/test_mhcnuggets_1.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,10 @@ nextflow_pipeline {
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/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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
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4 changes: 2 additions & 2 deletions tests/pipeline/test_mhcnuggets_2.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,10 @@ nextflow_pipeline {
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/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("$outputDir/figures/entity_binding_ratios.DPB1_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.DPB1_01_01.pdf").exists() },
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16 changes: 8 additions & 8 deletions tests/pipeline/test_mouse.nf.test
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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("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
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("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/WARNING_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/logs/download_proteins.log").exists() },
{ assert new File("$outputDir/logs/WARNING_unify_peptide_lengths.log").exists() },

{ assert new File("$outputDir/prodigal/proteins.pred_1.tsv.gz").exists() }
)
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4 changes: 2 additions & 2 deletions tests/pipeline/test_mouse_all_pep_lengths.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,10 @@ nextflow_pipeline {
path("$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("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$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("$outputDir/figures/entity_binding_ratios.H2-Db.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.H2-Db.pdf").exists() },
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16 changes: 8 additions & 8 deletions tests/pipeline/test_taxa_only.nf.test
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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("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
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("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },

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

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