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Update tests
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@fasterius
fasterius committed Jan 3, 2024
1 parent 70726cd commit 78963ce
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Showing 5 changed files with 12 additions and 38 deletions.
3 changes: 0 additions & 3 deletions tests/pipeline/test_downstream.nf.test
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Expand Up @@ -19,9 +19,6 @@ nextflow_pipeline {

// Data
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_processed.h5ad").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_norm.h5ad").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_plain.h5ad").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_raw.h5ad").exists() },

// Reports
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_qc_and_normalisation.html").text.contains("Distributions after filtering") },
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16 changes: 5 additions & 11 deletions tests/pipeline/test_spaceranger_ffpe_v1.nf.test
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Expand Up @@ -24,9 +24,6 @@ nextflow_pipeline {

// Data
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_processed.h5ad").exists() },
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_norm.h5ad").exists() },
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_plain.h5ad").exists() },
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_raw.h5ad").exists() },

// Reports
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/reports/st_qc_and_normalisation.html").text.contains("Distributions after filtering") },
Expand All @@ -37,20 +34,17 @@ nextflow_pipeline {
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/degs/st_spatial_de.csv").exists() },

// Space Ranger
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/web_summary.html").exists() },
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/web_summary.html").exists() },
{ assert snapshot(
path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/raw_feature_bc_matrix.h5"),
path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/filtered_feature_bc_matrix.h5"),
path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/raw_feature_bc_matrix.h5"),
path("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/filtered_feature_bc_matrix.h5"),
)},
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/raw_feature_bc_matrix.h5").exists() },
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/outs/spatial/tissue_positions.csv").exists() },
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/raw_feature_bc_matrix.h5").exists() },
{ assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/spaceranger/outs/spatial/tissue_positions.csv").exists() },

// MultiQC
{ assert file("$outputDir/multiqc/multiqc_report.html").text.contains("Visium_FFPE_Human_Ovarian_Cancer")}
)
}
}



}
9 changes: 1 addition & 8 deletions tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap
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13 changes: 5 additions & 8 deletions tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,6 @@ nextflow_pipeline {

// Data
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_processed.h5ad").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_norm.h5ad").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_plain.h5ad").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_raw.h5ad").exists() },

// Reports
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_qc_and_normalisation.html").text.contains("Distributions after filtering") },
Expand All @@ -37,13 +34,13 @@ nextflow_pipeline {
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/degs/st_spatial_de.csv").exists() },

// Space Ranger
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/web_summary.html").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/web_summary.html").exists() },
{ assert snapshot(
path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/raw_feature_bc_matrix.h5"),
path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/filtered_feature_bc_matrix.h5"),
path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/raw_feature_bc_matrix.h5"),
path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/filtered_feature_bc_matrix.h5"),
)},
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/raw_feature_bc_matrix.h5").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/outs/spatial/tissue_positions.csv").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/raw_feature_bc_matrix.h5").exists() },
{ assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/spaceranger/outs/spatial/tissue_positions.csv").exists() },

// MultiQC
{ assert file("$outputDir/multiqc/multiqc_report.html").text.contains("CytAssist_11mm_FFPE_Human_Glioblastoma_2_4")}
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9 changes: 1 addition & 8 deletions tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap
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