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Merged
nictru merged 1 commit into from
Jun 6, 2026
Merged

Centralize pipeline nf-test analysis plans and enable LIANA #293

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3 changes: 2 additions & 1 deletion nf-test.config
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Expand Up @@ -29,7 +29,8 @@ config {
'nf-test.config',
'tests/.nftignore',
'tests/nextflow.config',
'tests/analysis_plan_extension.csv',
'tests/analysis_plan.csv',
'tests/analysis_plan_sub.csv',
]

// load the necessary plugins
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2 changes: 1 addition & 1 deletion tests/analysis_plan_extension.csv → tests/analysis_plan.csv
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@@ -1,2 +1,2 @@
integration,subset,resolution,analyses
scvi,global,0.5,"paga,de"
scvi,global,0.5,"paga,liana,de"
3 changes: 3 additions & 0 deletions tests/analysis_plan_sub.csv
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@@ -0,0 +1,3 @@
integration,subset,resolution,analyses
scvi,,0.5,"paga,liana,de"
scvi,,1.0,"paga,liana,de"
22 changes: 1 addition & 21 deletions tests/default.nf.test.snap
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Expand Up @@ -222,36 +222,16 @@
"celltypes/singler/SRR28679758_singler_predictions.csv",
"cluster_dimred",
"cluster_dimred/bbknn",
"cluster_dimred/bbknn/entropy",
"cluster_dimred/bbknn/entropy/bbknn-global-0.5_entropy.png",
"cluster_dimred/bbknn/entropy/bbknn-global-1.0_entropy.png",
"cluster_dimred/bbknn/leiden",
"cluster_dimred/bbknn/leiden/bbknn-global-0.5_leiden.png",
"cluster_dimred/bbknn/leiden/bbknn-global-1.0_leiden.png",
"cluster_dimred/bbknn/umap",
"cluster_dimred/combat",
"cluster_dimred/combat/entropy",
"cluster_dimred/combat/entropy/combat-global-0.5_entropy.png",
"cluster_dimred/combat/entropy/combat-global-1.0_entropy.png",
"cluster_dimred/combat/leiden",
"cluster_dimred/combat/leiden/combat-global-0.5_leiden.png",
"cluster_dimred/combat/leiden/combat-global-1.0_leiden.png",
"cluster_dimred/combat/umap",
"cluster_dimred/scvi",
"cluster_dimred/scvi/entropy",
"cluster_dimred/scvi/entropy/scvi-global-0.5_entropy.png",
"cluster_dimred/scvi/entropy/scvi-global-1.0_entropy.png",
"cluster_dimred/scvi/leiden",
"cluster_dimred/scvi/leiden/scvi-global-0.5_leiden.png",
"cluster_dimred/scvi/leiden/scvi-global-1.0_leiden.png",
"cluster_dimred/scvi/umap",
"cluster_dimred/symphony",
"cluster_dimred/symphony/entropy",
"cluster_dimred/symphony/entropy/symphony-global-0.5_entropy.png",
"cluster_dimred/symphony/entropy/symphony-global-1.0_entropy.png",
"cluster_dimred/symphony/leiden",
"cluster_dimred/symphony/leiden/symphony-global-0.5_leiden.png",
"cluster_dimred/symphony/leiden/symphony-global-1.0_leiden.png",
"cluster_dimred/symphony/umap",
"combine",
"combine/integrate",
Expand Down Expand Up @@ -307,7 +287,7 @@
"qc-report.qmd:md5,13061014a897b3fbdafd6ea3212df0e0"
]
],
"timestamp": "2026-05-28T17:09:18.020969587",
"timestamp": "2026-06-06T15:16:05.937543361",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.04.0"
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28 changes: 1 addition & 27 deletions tests/main_pipeline_build.nf.test.snap
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Expand Up @@ -224,44 +224,18 @@
"celltypes/singler/SRR28679758_singler_predictions.csv",
"cluster_dimred",
"cluster_dimred/bbknn",
"cluster_dimred/bbknn/entropy",
"cluster_dimred/bbknn/entropy/bbknn-global-0.5_entropy.png",
"cluster_dimred/bbknn/entropy/bbknn-global-1.0_entropy.png",
"cluster_dimred/bbknn/leiden",
"cluster_dimred/bbknn/leiden/bbknn-global-0.5_leiden.png",
"cluster_dimred/bbknn/leiden/bbknn-global-1.0_leiden.png",
"cluster_dimred/bbknn/umap",
"cluster_dimred/combat",
"cluster_dimred/combat/entropy",
"cluster_dimred/combat/entropy/combat-global-0.5_entropy.png",
"cluster_dimred/combat/entropy/combat-global-1.0_entropy.png",
"cluster_dimred/combat/leiden",
"cluster_dimred/combat/leiden/combat-global-0.5_leiden.png",
"cluster_dimred/combat/leiden/combat-global-1.0_leiden.png",
"cluster_dimred/combat/umap",
"cluster_dimred/scvi",
"cluster_dimred/scvi/entropy",
"cluster_dimred/scvi/entropy/scvi-global-0.5_entropy.png",
"cluster_dimred/scvi/entropy/scvi-global-1.0_entropy.png",
"cluster_dimred/scvi/leiden",
"cluster_dimred/scvi/leiden/scvi-global-0.5_leiden.png",
"cluster_dimred/scvi/leiden/scvi-global-1.0_leiden.png",
"cluster_dimred/scvi/umap",
"cluster_dimred/seurat",
"cluster_dimred/seurat/entropy",
"cluster_dimred/seurat/entropy/seurat-global-0.5_entropy.png",
"cluster_dimred/seurat/entropy/seurat-global-1.0_entropy.png",
"cluster_dimred/seurat/leiden",
"cluster_dimred/seurat/leiden/seurat-global-0.5_leiden.png",
"cluster_dimred/seurat/leiden/seurat-global-1.0_leiden.png",
"cluster_dimred/seurat/umap",
"cluster_dimred/symphony",
"cluster_dimred/symphony/entropy",
"cluster_dimred/symphony/entropy/symphony-global-0.5_entropy.png",
"cluster_dimred/symphony/entropy/symphony-global-1.0_entropy.png",
"cluster_dimred/symphony/leiden",
"cluster_dimred/symphony/leiden/symphony-global-0.5_leiden.png",
"cluster_dimred/symphony/leiden/symphony-global-1.0_leiden.png",
"cluster_dimred/symphony/umap",
"combine",
"combine/integrate",
Expand Down Expand Up @@ -318,7 +292,7 @@
"qc-report.qmd:md5,13061014a897b3fbdafd6ea3212df0e0"
]
],
"timestamp": "2026-05-31T12:35:21.295737307",
"timestamp": "2026-06-06T15:16:14.553425954",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.04.0"
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1 change: 0 additions & 1 deletion tests/main_pipeline_extend.nf.test
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Expand Up @@ -18,7 +18,6 @@ nextflow_pipeline {
scvi_model = pipelines_testdata_base_path + 'extension_base/model.pt'
symphony_reference = pipelines_testdata_base_path + 'extension_base/symphony_reference.h5ad'
base_adata = pipelines_testdata_base_path + 'extension_base/merged.h5ad'
analysis_plan = "${projectDir}/tests/analysis_plan_extension.csv"
}
}

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10 changes: 1 addition & 9 deletions tests/main_pipeline_reference_mapping.nf.test.snap
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Expand Up @@ -184,18 +184,10 @@
"cluster_dimred/scvi",
"cluster_dimred/scvi/entropy",
"cluster_dimred/scvi/entropy/scvi-global-0.5_entropy.png",
"cluster_dimred/scvi/entropy/scvi-global-1.0_entropy.png",
"cluster_dimred/scvi/leiden",
"cluster_dimred/scvi/leiden/scvi-global-0.5_leiden.png",
"cluster_dimred/scvi/leiden/scvi-global-1.0_leiden.png",
"cluster_dimred/scvi/umap",
"cluster_dimred/symphony",
"cluster_dimred/symphony/entropy",
"cluster_dimred/symphony/entropy/symphony-global-0.5_entropy.png",
"cluster_dimred/symphony/entropy/symphony-global-1.0_entropy.png",
"cluster_dimred/symphony/leiden",
"cluster_dimred/symphony/leiden/symphony-global-0.5_leiden.png",
"cluster_dimred/symphony/leiden/symphony-global-1.0_leiden.png",
"cluster_dimred/symphony/umap",
"combine",
"combine/integrate",
Expand Down Expand Up @@ -243,7 +235,7 @@
"qc-report.qmd:md5,13061014a897b3fbdafd6ea3212df0e0"
]
],
"timestamp": "2026-05-29T14:31:02.484302876",
"timestamp": "2026-06-06T15:07:48.478900584",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.04.0"
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3 changes: 2 additions & 1 deletion tests/main_pipeline_sub.nf.test
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Expand Up @@ -12,10 +12,11 @@ nextflow_pipeline {
outdir = "$outputDir"
input = null
base_adata = pipelines_testdata_base_path + 'extension_base/merged.h5ad'
base_embeddings = 'symphony'
base_embeddings = 'scvi'
cluster_global = false
cluster_per_label = true
base_label_col = 'sample'
analysis_plan = "${projectDir}/tests/analysis_plan_sub.csv"
}
}

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36 changes: 18 additions & 18 deletions tests/main_pipeline_sub.nf.test.snap
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Expand Up @@ -59,24 +59,24 @@
},
[
"adata",
"adata/symphony.h5ad",
"adata/scvi.h5ad",
"cluster_dimred",
"cluster_dimred/symphony",
"cluster_dimred/symphony/entropy",
"cluster_dimred/symphony/entropy/symphony-SRR28679756-0.5_entropy.png",
"cluster_dimred/symphony/entropy/symphony-SRR28679756-1.0_entropy.png",
"cluster_dimred/symphony/entropy/symphony-SRR28679757-0.5_entropy.png",
"cluster_dimred/symphony/entropy/symphony-SRR28679757-1.0_entropy.png",
"cluster_dimred/symphony/entropy/symphony-SRR28679758-0.5_entropy.png",
"cluster_dimred/symphony/entropy/symphony-SRR28679758-1.0_entropy.png",
"cluster_dimred/symphony/leiden",
"cluster_dimred/symphony/leiden/symphony-SRR28679756-0.5_leiden.png",
"cluster_dimred/symphony/leiden/symphony-SRR28679756-1.0_leiden.png",
"cluster_dimred/symphony/leiden/symphony-SRR28679757-0.5_leiden.png",
"cluster_dimred/symphony/leiden/symphony-SRR28679757-1.0_leiden.png",
"cluster_dimred/symphony/leiden/symphony-SRR28679758-0.5_leiden.png",
"cluster_dimred/symphony/leiden/symphony-SRR28679758-1.0_leiden.png",
"cluster_dimred/symphony/umap",
"cluster_dimred/scvi",
"cluster_dimred/scvi/entropy",
"cluster_dimred/scvi/entropy/scvi-SRR28679756-0.5_entropy.png",
"cluster_dimred/scvi/entropy/scvi-SRR28679756-1.0_entropy.png",
"cluster_dimred/scvi/entropy/scvi-SRR28679757-0.5_entropy.png",
"cluster_dimred/scvi/entropy/scvi-SRR28679757-1.0_entropy.png",
"cluster_dimred/scvi/entropy/scvi-SRR28679758-0.5_entropy.png",
"cluster_dimred/scvi/entropy/scvi-SRR28679758-1.0_entropy.png",
"cluster_dimred/scvi/leiden",
"cluster_dimred/scvi/leiden/scvi-SRR28679756-0.5_leiden.png",
"cluster_dimred/scvi/leiden/scvi-SRR28679756-1.0_leiden.png",
"cluster_dimred/scvi/leiden/scvi-SRR28679757-0.5_leiden.png",
"cluster_dimred/scvi/leiden/scvi-SRR28679757-1.0_leiden.png",
"cluster_dimred/scvi/leiden/scvi-SRR28679758-0.5_leiden.png",
"cluster_dimred/scvi/leiden/scvi-SRR28679758-1.0_leiden.png",
"cluster_dimred/scvi/umap",
"finalized",
"finalized/base.h5ad",
"finalized/base.rds",
Expand Down Expand Up @@ -111,7 +111,7 @@
"qc-report.qmd:md5,13061014a897b3fbdafd6ea3212df0e0"
]
],
"timestamp": "2026-05-29T14:32:12.630005788",
"timestamp": "2026-06-06T15:32:56.788142055",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.04.0"
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1 change: 1 addition & 0 deletions tests/nextflow.config
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Expand Up @@ -9,6 +9,7 @@
params {
modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nictru/test-datasets/97addfb0946c0e51dbb70ee1391142d12e70f085/'
analysis_plan = "${projectDir}/tests/analysis_plan.csv"
// CyteType is slow (remote LLM API); module nf-tests cover it — keep off in pipeline/subworkflow nf-tests
cytetype_study_context = ''
}
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