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Bugfix/figure creation #129

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merged 2 commits into from
Aug 7, 2024
Merged

Bugfix/figure creation #129

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d0711e6
fix plot generation
tillenglert Aug 6, 2024
890b4a1
add figures to tests
tillenglert Aug 6, 2024
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2 changes: 1 addition & 1 deletion modules/local/plot_entity_binding_ratios.nf
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Expand Up @@ -9,7 +9,7 @@ process PLOT_ENTITY_BINDING_RATIOS {
publishDir "${params.outdir}/figures", mode: params.publish_dir_mode

input:
path prep_entity_binding_ratios
each path(prep_entity_binding_ratios)
path alleles

output:
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2 changes: 1 addition & 1 deletion modules/local/plot_score_distribution.nf
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Expand Up @@ -7,7 +7,7 @@ process PLOT_SCORE_DISTRIBUTION {
'biocontainers/bioconductor-alphabeta:1.8.0--r41hdfd78af_0' }"

input:
path prep_scores
each path(prep_scores)
path alleles
path conditions

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3 changes: 3 additions & 0 deletions tests/pipeline/test.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ 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("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() },
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3 changes: 3 additions & 0 deletions tests/pipeline/test_all.nf.test
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Expand Up @@ -39,6 +39,9 @@ nextflow_pipeline {
{ assert new File("$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 new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },
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3 changes: 3 additions & 0 deletions tests/pipeline/test_assembly_only.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ 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("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
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3 changes: 3 additions & 0 deletions tests/pipeline/test_bins_only.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ assert new File("$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 new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$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() }
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3 changes: 3 additions & 0 deletions tests/pipeline/test_coassembly.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ 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("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() },
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3 changes: 3 additions & 0 deletions tests/pipeline/test_mhcflurry.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ assert new File("$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 new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
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3 changes: 3 additions & 0 deletions tests/pipeline/test_mhcnuggets_1.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ assert new File("$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 new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
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3 changes: 3 additions & 0 deletions tests/pipeline/test_mhcnuggets_2.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ assert new File("$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 new File("$outputDir/figures/entity_binding_ratios.DQB1_02_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.DQB1_02_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.DQB1_02_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
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3 changes: 3 additions & 0 deletions tests/pipeline/test_mouse.nf.test
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Expand Up @@ -39,6 +39,9 @@ nextflow_pipeline {
{ assert new File("$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 new File("$outputDir/figures/entity_binding_ratios.H2-Ld.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.H2-Ld.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.H2-Ld.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/WARNING_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },
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3 changes: 3 additions & 0 deletions tests/pipeline/test_mouse_all_pep_lengths.nf.test
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Expand Up @@ -35,6 +35,9 @@ nextflow_pipeline {
{ 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("$outputDir/figures/prediction_score_distribution.H2-Db.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.H2-Ld.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.H2-Ld.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.H2-Ld.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
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3 changes: 3 additions & 0 deletions tests/pipeline/test_taxa_only.nf.test
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Expand Up @@ -39,6 +39,9 @@ nextflow_pipeline {
{ 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("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },
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3 changes: 3 additions & 0 deletions tests/pipeline/test_taxa_specific_assembly.nf.test
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Expand Up @@ -39,6 +39,9 @@ nextflow_pipeline {
{ assert new File("$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 new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },
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