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remove bank lines from *.nf.test
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@tillenglert
tillenglert committed Aug 6, 2024
1 parent e431d5b commit 707375c
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Showing 12 changed files with 0 additions and 60 deletions.
4 changes: 0 additions & 4 deletions tests/pipeline/test.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ nextflow_pipeline {
{ assert workflow.success },
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -33,14 +32,11 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log"),
path("$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() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.tsv.gz").exists() }
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5 changes: 0 additions & 5 deletions tests/pipeline/test_all.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ nextflow_pipeline {
{ assert workflow.success },
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -33,20 +32,16 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },

{ 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("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() },
{ assert new File("$outputDir/entrez_data/taxa_assemblies.tsv").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("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },

{ 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() },
{ assert new File("$outputDir/prodigal/proteins.pred_2.tsv.gz").exists() }
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5 changes: 0 additions & 5 deletions tests/pipeline/test_assembly_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,14 +32,11 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },

{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
}
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5 changes: 0 additions & 5 deletions tests/pipeline/test_bins_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,14 +32,11 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },

{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() }
)
}
Expand Down
5 changes: 0 additions & 5 deletions tests/pipeline/test_coassembly.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,14 +32,11 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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("$outputDir/logs/prediction_warnings.log"),
path("$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() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.2.tsv.gz").exists() }
Expand Down
5 changes: 0 additions & 5 deletions tests/pipeline/test_mhcflurry.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,13 +32,10 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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/prodigal/proteins.pred_0.tsv.gz").exists() }
)
}
Expand Down
5 changes: 0 additions & 5 deletions tests/pipeline/test_mhcnuggets_1.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,13 +32,10 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$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/prodigal/proteins.pred_0.tsv.gz").exists() }
)
}
Expand Down
5 changes: 0 additions & 5 deletions tests/pipeline/test_mhcnuggets_2.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,13 +32,10 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.DPB1_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.DPB1_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.DPB1_01_01.pdf").exists() },

{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },

{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
}
Expand Down
6 changes: 0 additions & 6 deletions tests/pipeline/test_mouse.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,20 +32,16 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },

{ 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("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() },
{ assert new File("$outputDir/entrez_data/taxa_assemblies.tsv").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() },
{ assert new File("$outputDir/figures/prediction_score_distribution.H2-Db.pdf").exists() },

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

{ assert new File("$outputDir/prodigal/proteins.pred_1.tsv.gz").exists() }
)
}
Expand Down
5 changes: 0 additions & 5 deletions tests/pipeline/test_mouse_all_pep_lengths.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,13 +32,10 @@ nextflow_pipeline {
path("$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("$outputDir/figures/entity_binding_ratios.H2-Db.pdf").exists() },
{ assert new File("$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 new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
}
Expand Down
5 changes: 0 additions & 5 deletions tests/pipeline/test_taxa_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,16 +32,13 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },

{ 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("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() },
{ assert new File("$outputDir/entrez_data/taxa_assemblies.tsv").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("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },
Expand Down
5 changes: 0 additions & 5 deletions tests/pipeline/test_taxa_specific_assembly.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },

{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
Expand All @@ -34,16 +32,13 @@ nextflow_pipeline {
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },

{ 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("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() },
{ assert new File("$outputDir/entrez_data/taxa_assemblies.tsv").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("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },
Expand Down

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