diff --git a/tests/pipeline/test.nf.test b/tests/pipeline/test.nf.test
index 6d1934d4..a1593bf7 100644
--- a/tests/pipeline/test.nf.test
+++ b/tests/pipeline/test.nf.test
@@ -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() },
diff --git a/tests/pipeline/test_all.nf.test b/tests/pipeline/test_all.nf.test
index f2b78899..c579d301 100644
--- a/tests/pipeline/test_all.nf.test
+++ b/tests/pipeline/test_all.nf.test
@@ -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() },
@@ -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() },
diff --git a/tests/pipeline/test_assembly_only.nf.test b/tests/pipeline/test_assembly_only.nf.test
index 623d28d7..beefd0ba 100644
--- a/tests/pipeline/test_assembly_only.nf.test
+++ b/tests/pipeline/test_assembly_only.nf.test
@@ -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("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
             )
diff --git a/tests/pipeline/test_bins_only.nf.test b/tests/pipeline/test_bins_only.nf.test
index 96cd2a67..4bc30a19 100644
--- a/tests/pipeline/test_bins_only.nf.test
+++ b/tests/pipeline/test_bins_only.nf.test
@@ -30,17 +30,17 @@ nextflow_pipeline {
                                 path("$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("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() }
             )
diff --git a/tests/pipeline/test_coassembly.nf.test b/tests/pipeline/test_coassembly.nf.test
index 8073d3e6..b1152561 100644
--- a/tests/pipeline/test_coassembly.nf.test
+++ b/tests/pipeline/test_coassembly.nf.test
@@ -30,17 +30,17 @@ nextflow_pipeline {
                                 path("$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() },
diff --git a/tests/pipeline/test_mhcflurry.nf.test b/tests/pipeline/test_mhcflurry.nf.test
index 46a1da19..7acdd085 100644
--- a/tests/pipeline/test_mhcflurry.nf.test
+++ b/tests/pipeline/test_mhcflurry.nf.test
@@ -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() },
diff --git a/tests/pipeline/test_mhcnuggets_1.nf.test b/tests/pipeline/test_mhcnuggets_1.nf.test
index 6e2278fe..3a4b25d4 100644
--- a/tests/pipeline/test_mhcnuggets_1.nf.test
+++ b/tests/pipeline/test_mhcnuggets_1.nf.test
@@ -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() },
diff --git a/tests/pipeline/test_mhcnuggets_2.nf.test b/tests/pipeline/test_mhcnuggets_2.nf.test
index 9fc0008e..54844431 100644
--- a/tests/pipeline/test_mhcnuggets_2.nf.test
+++ b/tests/pipeline/test_mhcnuggets_2.nf.test
@@ -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() },
diff --git a/tests/pipeline/test_mouse.nf.test b/tests/pipeline/test_mouse.nf.test
index baeb08ec..aa4a52d7 100644
--- a/tests/pipeline/test_mouse.nf.test
+++ b/tests/pipeline/test_mouse.nf.test
@@ -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() },
@@ -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("$outputDir/prodigal/proteins.pred_1.tsv.gz").exists() }
             )
diff --git a/tests/pipeline/test_mouse_all_pep_lengths.nf.test b/tests/pipeline/test_mouse_all_pep_lengths.nf.test
index 36a2a79b..447e7a9f 100644
--- a/tests/pipeline/test_mouse_all_pep_lengths.nf.test
+++ b/tests/pipeline/test_mouse_all_pep_lengths.nf.test
@@ -30,10 +30,10 @@ nextflow_pipeline {
                                 path("$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() },
diff --git a/tests/pipeline/test_taxa_only.nf.test b/tests/pipeline/test_taxa_only.nf.test
index 521f2671..a7f1fb3a 100644
--- a/tests/pipeline/test_taxa_only.nf.test
+++ b/tests/pipeline/test_taxa_only.nf.test
@@ -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() },
@@ -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() }
             )
         }
 
diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test b/tests/pipeline/test_taxa_specific_assembly.nf.test
index 47bb88ff..8a1489ab 100644
--- a/tests/pipeline/test_taxa_specific_assembly.nf.test
+++ b/tests/pipeline/test_taxa_specific_assembly.nf.test
@@ -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 snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") },
                 { assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() },
@@ -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() }
             )
         }