diff --git a/nf-test.config b/nf-test.config index c56bd5d9..050d70f6 100644 --- a/nf-test.config +++ b/nf-test.config @@ -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 diff --git a/tests/analysis_plan_extension.csv b/tests/analysis_plan.csv similarity index 54% rename from tests/analysis_plan_extension.csv rename to tests/analysis_plan.csv index 12e1f53e..dc39c197 100644 --- a/tests/analysis_plan_extension.csv +++ b/tests/analysis_plan.csv @@ -1,2 +1,2 @@ integration,subset,resolution,analyses -scvi,global,0.5,"paga,de" +scvi,global,0.5,"paga,liana,de" diff --git a/tests/analysis_plan_sub.csv b/tests/analysis_plan_sub.csv new file mode 100644 index 00000000..951a4361 --- /dev/null +++ b/tests/analysis_plan_sub.csv @@ -0,0 +1,3 @@ +integration,subset,resolution,analyses +scvi,,0.5,"paga,liana,de" +scvi,,1.0,"paga,liana,de" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5fc73379..a58958c6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -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", @@ -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" diff --git a/tests/main_pipeline_build.nf.test.snap b/tests/main_pipeline_build.nf.test.snap index f7cb9baa..fced8405 100644 --- a/tests/main_pipeline_build.nf.test.snap +++ b/tests/main_pipeline_build.nf.test.snap @@ -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", @@ -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" diff --git a/tests/main_pipeline_extend.nf.test b/tests/main_pipeline_extend.nf.test index 2195b716..7126bb60 100644 --- a/tests/main_pipeline_extend.nf.test +++ b/tests/main_pipeline_extend.nf.test @@ -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 = "${projectDir}/tests/analysis_plan_extension.csv" } } diff --git a/tests/main_pipeline_reference_mapping.nf.test.snap b/tests/main_pipeline_reference_mapping.nf.test.snap index e8795e97..00fb5ace 100644 --- a/tests/main_pipeline_reference_mapping.nf.test.snap +++ b/tests/main_pipeline_reference_mapping.nf.test.snap @@ -184,18 +184,10 @@ "cluster_dimred/scvi", "cluster_dimred/scvi/entropy", "cluster_dimred/scvi/entropy/scvi-global-0.5_entropy.png", - "cluster_dimred/scvi/entropy/scvi-global-1.0_entropy.png", "cluster_dimred/scvi/leiden", "cluster_dimred/scvi/leiden/scvi-global-0.5_leiden.png", - "cluster_dimred/scvi/leiden/scvi-global-1.0_leiden.png", "cluster_dimred/scvi/umap", "cluster_dimred/symphony", - "cluster_dimred/symphony/entropy", - "cluster_dimred/symphony/entropy/symphony-global-0.5_entropy.png", - "cluster_dimred/symphony/entropy/symphony-global-1.0_entropy.png", - "cluster_dimred/symphony/leiden", - "cluster_dimred/symphony/leiden/symphony-global-0.5_leiden.png", - "cluster_dimred/symphony/leiden/symphony-global-1.0_leiden.png", "cluster_dimred/symphony/umap", "combine", "combine/integrate", @@ -243,7 +235,7 @@ "qc-report.qmd:md5,13061014a897b3fbdafd6ea3212df0e0" ] ], - "timestamp": "2026-05-29T14:31:02.484302876", + "timestamp": "2026-06-06T15:07:48.478900584", "meta": { "nf-test": "0.9.4", "nextflow": "26.04.0" diff --git a/tests/main_pipeline_sub.nf.test b/tests/main_pipeline_sub.nf.test index 03758609..0e6f6228 100644 --- a/tests/main_pipeline_sub.nf.test +++ b/tests/main_pipeline_sub.nf.test @@ -12,10 +12,11 @@ nextflow_pipeline { outdir = "$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" } } diff --git a/tests/main_pipeline_sub.nf.test.snap b/tests/main_pipeline_sub.nf.test.snap index cb74498d..37e6c418 100644 --- a/tests/main_pipeline_sub.nf.test.snap +++ b/tests/main_pipeline_sub.nf.test.snap @@ -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", @@ -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" diff --git a/tests/nextflow.config b/tests/nextflow.config index 0ab28b9b..7c37f310 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -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 = '' }