From fd1e70c4c3024d50b01f7a25334294c92acb8380 Mon Sep 17 00:00:00 2001 From: Christophe Avenel Date: Sun, 11 Oct 2026 23:39:59 +0200 Subject: [PATCH 1/7] Update local modules to the spatialdata 0.8 stack Reading Space Ranger's segmented outputs needs spatialdata-io >= 0.7, which brings spatialdata 0.8, anndata 0.13 and a newer pandas. Move all local modules to one image built on that stack, and fix what breaks under it: - ADATA_EXTEND: anndata 0.13 reports an empty `layers` group as a single `None` key, so count only real keys. - update_table: newer pandas rejects element-wise assignment of mixed values into a float64 column. Assign the whole column with rename/reindex. - nf-test: nft-anndata 0.4.1 cannot read categoricals written by anndata 0.13; update to 0.5.2. --- conf/modules.config | 6 +++--- modules/local/adata/extend/main.nf | 2 +- modules/local/adata/extend/templates/extend.py | 3 ++- modules/local/adata/merge/main.nf | 2 +- modules/local/scanpy/calculate_qc_metrics/main.nf | 2 +- modules/local/scanpy/filter/main.nf | 2 +- modules/local/scanpy/harmony/main.nf | 2 +- modules/local/scanpy/highly_variable_genes/main.nf | 2 +- modules/local/scanpy/leiden/main.nf | 2 +- modules/local/scanpy/log1p/main.nf | 2 +- modules/local/scanpy/neighbors/main.nf | 2 +- modules/local/scanpy/normalize_total/main.nf | 2 +- modules/local/scanpy/pca/main.nf | 2 +- modules/local/scanpy/rank_genes_groups/main.nf | 2 +- modules/local/scanpy/scanorama/main.nf | 2 +- modules/local/scanpy/umap/main.nf | 2 +- modules/local/sdata/merge/main.nf | 2 +- modules/local/sdata/read_visium/main.nf | 2 +- modules/local/sdata/to_legacy_anndata/main.nf | 2 +- modules/local/sdata/update_table/main.nf | 2 +- .../local/sdata/update_table/templates/update_table.py | 8 ++------ modules/local/squidpy/interaction_matrix/main.nf | 2 +- modules/local/squidpy/nhood_enrichment/main.nf | 2 +- modules/local/squidpy/spatial_autocorr/main.nf | 2 +- modules/local/squidpy/spatial_neighbors/main.nf | 2 +- nf-test.config | 2 +- tests/helpers/duplicate_var_names.nf | 2 +- 27 files changed, 31 insertions(+), 34 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 32cfd0d0..22ecf1a9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -83,11 +83,11 @@ process { // The Seqera image used in multiple modules of this pipeline contains many // different packages, the build information for which you can find here: - // https://wave.seqera.io/view/builds/bd-95f731fde0b9ddef_1. + // https://wave.seqera.io/view/builds/bd-d457f4c6ebb7b325_1. withName: REPORT { ext.prefix = { "${notebook.baseName}-${meta.id}" } ext.args = { "--metadata subtitle:'Sample: ${meta.id}'" } - container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef' + container = 'community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325' publishDir = [ path: { "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, @@ -137,7 +137,7 @@ process { withName: REPORT_INTEGRATED { ext.prefix = { "${notebook.baseName}" } - container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef' + container = 'community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325' publishDir = [ path: { "${params.outdir}/integration" }, mode: params.publish_dir_mode, diff --git a/modules/local/adata/extend/main.nf b/modules/local/adata/extend/main.nf index 5c6256f3..97b64543 100644 --- a/modules/local/adata/extend/main.nf +++ b/modules/local/adata/extend/main.nf @@ -2,7 +2,7 @@ process ADATA_EXTEND { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple ( diff --git a/modules/local/adata/extend/templates/extend.py b/modules/local/adata/extend/templates/extend.py index 674a290e..14738c33 100644 --- a/modules/local/adata/extend/templates/extend.py +++ b/modules/local/adata/extend/templates/extend.py @@ -80,7 +80,8 @@ def load_layer(path): if slot in ("obs", "var"): n_entries = len(content.columns) else: - n_entries = len(content) + # anndata >= 0.13 reports an empty `layers` group as one `None` key + n_entries = len([k for k in content if k is not None]) if n_entries > 0: non_empty.append(f"`{slot}`") if non_empty: diff --git a/modules/local/adata/merge/main.nf b/modules/local/adata/merge/main.nf index b3b17d39..23c69f37 100644 --- a/modules/local/adata/merge/main.nf +++ b/modules/local/adata/merge/main.nf @@ -1,7 +1,7 @@ process ADATA_MERGE { label 'process_low' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: path(h5ad, arity: '1..*') diff --git a/modules/local/scanpy/calculate_qc_metrics/main.nf b/modules/local/scanpy/calculate_qc_metrics/main.nf index 26850110..d71b5721 100644 --- a/modules/local/scanpy/calculate_qc_metrics/main.nf +++ b/modules/local/scanpy/calculate_qc_metrics/main.nf @@ -2,7 +2,7 @@ process SCANPY_CALCULATE_QC_METRICS { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/filter/main.nf b/modules/local/scanpy/filter/main.nf index 7929c1a5..a62849d1 100644 --- a/modules/local/scanpy/filter/main.nf +++ b/modules/local/scanpy/filter/main.nf @@ -2,7 +2,7 @@ process SCANPY_FILTER { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/harmony/main.nf b/modules/local/scanpy/harmony/main.nf index 46d2f4e6..1cac1f3e 100644 --- a/modules/local/scanpy/harmony/main.nf +++ b/modules/local/scanpy/harmony/main.nf @@ -2,7 +2,7 @@ process SCANPY_HARMONY { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(h5ad, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/highly_variable_genes/main.nf b/modules/local/scanpy/highly_variable_genes/main.nf index 4076986d..6a572d10 100644 --- a/modules/local/scanpy/highly_variable_genes/main.nf +++ b/modules/local/scanpy/highly_variable_genes/main.nf @@ -2,7 +2,7 @@ process SCANPY_HIGHLY_VARIABLE_GENES { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(h5ad, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/leiden/main.nf b/modules/local/scanpy/leiden/main.nf index 2a1009ea..0b1f7698 100644 --- a/modules/local/scanpy/leiden/main.nf +++ b/modules/local/scanpy/leiden/main.nf @@ -2,7 +2,7 @@ process SCANPY_LEIDEN { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(h5ad, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/log1p/main.nf b/modules/local/scanpy/log1p/main.nf index 4be53c2e..529c532b 100644 --- a/modules/local/scanpy/log1p/main.nf +++ b/modules/local/scanpy/log1p/main.nf @@ -2,7 +2,7 @@ process SCANPY_LOG1P { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/neighbors/main.nf b/modules/local/scanpy/neighbors/main.nf index 2aaba7cb..04b78f11 100644 --- a/modules/local/scanpy/neighbors/main.nf +++ b/modules/local/scanpy/neighbors/main.nf @@ -2,7 +2,7 @@ process SCANPY_NEIGHBORS { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/normalize_total/main.nf b/modules/local/scanpy/normalize_total/main.nf index 82d9a18e..73c622b0 100644 --- a/modules/local/scanpy/normalize_total/main.nf +++ b/modules/local/scanpy/normalize_total/main.nf @@ -2,7 +2,7 @@ process SCANPY_NORMALIZE_TOTAL { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/pca/main.nf b/modules/local/scanpy/pca/main.nf index 15d712d2..b4090ba1 100644 --- a/modules/local/scanpy/pca/main.nf +++ b/modules/local/scanpy/pca/main.nf @@ -2,7 +2,7 @@ process SCANPY_PCA { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/rank_genes_groups/main.nf b/modules/local/scanpy/rank_genes_groups/main.nf index 8aeb08ae..85cc0054 100644 --- a/modules/local/scanpy/rank_genes_groups/main.nf +++ b/modules/local/scanpy/rank_genes_groups/main.nf @@ -2,7 +2,7 @@ process SCANPY_RANK_GENES_GROUPS { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/scanorama/main.nf b/modules/local/scanpy/scanorama/main.nf index 21f94597..b5f669db 100644 --- a/modules/local/scanpy/scanorama/main.nf +++ b/modules/local/scanpy/scanorama/main.nf @@ -2,7 +2,7 @@ process SCANPY_SCANORAMA { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(h5ad, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/scanpy/umap/main.nf b/modules/local/scanpy/umap/main.nf index 75efe7a0..e5f0e36a 100644 --- a/modules/local/scanpy/umap/main.nf +++ b/modules/local/scanpy/umap/main.nf @@ -2,7 +2,7 @@ process SCANPY_UMAP { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/sdata/merge/main.nf b/modules/local/sdata/merge/main.nf index 5ffac04f..cec2b768 100644 --- a/modules/local/sdata/merge/main.nf +++ b/modules/local/sdata/merge/main.nf @@ -1,7 +1,7 @@ process SDATA_MERGE { label 'process_low' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: path(sdata, stageAs: "?/*", arity: '1..*') diff --git a/modules/local/sdata/read_visium/main.nf b/modules/local/sdata/read_visium/main.nf index fccb4c2d..a0a5e860 100644 --- a/modules/local/sdata/read_visium/main.nf +++ b/modules/local/sdata/read_visium/main.nf @@ -2,7 +2,7 @@ process SDATA_READ_VISIUM { tag "${meta.id}" label 'process_low' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(spaceranger_dir, arity: '1') diff --git a/modules/local/sdata/to_legacy_anndata/main.nf b/modules/local/sdata/to_legacy_anndata/main.nf index 47cbe852..07be6c29 100644 --- a/modules/local/sdata/to_legacy_anndata/main.nf +++ b/modules/local/sdata/to_legacy_anndata/main.nf @@ -2,7 +2,7 @@ process SDATA_TO_LEGACY_ANNDATA { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(sdata, arity: '1') diff --git a/modules/local/sdata/update_table/main.nf b/modules/local/sdata/update_table/main.nf index 26320ae4..a950e0e5 100644 --- a/modules/local/sdata/update_table/main.nf +++ b/modules/local/sdata/update_table/main.nf @@ -2,7 +2,7 @@ process SDATA_UPDATE_TABLE { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(sdata, stageAs: "input.zarr", arity: '1'), path(adata, arity: '1') diff --git a/modules/local/sdata/update_table/templates/update_table.py b/modules/local/sdata/update_table/templates/update_table.py index 0101ee0c..eee61e80 100644 --- a/modules/local/sdata/update_table/templates/update_table.py +++ b/modules/local/sdata/update_table/templates/update_table.py @@ -255,12 +255,8 @@ def update_tables_from_concat(sdata, adata_concat, library_key): new_cols = set(adata_subset.obs.columns) - set(table.obs.columns) - skip for col in new_cols: - table.obs[col] = np.nan - for i, new_idx in enumerate(adata_subset.obs_names): - orig_idx = index_map[new_idx] - if orig_idx in table.obs_names: - table.obs.loc[orig_idx, col] = adata_subset.obs.iloc[i][col] - + values = adata_subset.obs[col].rename(index=index_map) + table.obs[col] = values.reindex(table.obs_names) logger.info(f" Added obs['{col}']") # ----------------------------------------------------------------------------- diff --git a/modules/local/squidpy/interaction_matrix/main.nf b/modules/local/squidpy/interaction_matrix/main.nf index b42b3a99..155b9c8a 100644 --- a/modules/local/squidpy/interaction_matrix/main.nf +++ b/modules/local/squidpy/interaction_matrix/main.nf @@ -2,7 +2,7 @@ process SQUIDPY_INTERACTION_MATRIX { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/squidpy/nhood_enrichment/main.nf b/modules/local/squidpy/nhood_enrichment/main.nf index 070d5d9f..cd2367b3 100644 --- a/modules/local/squidpy/nhood_enrichment/main.nf +++ b/modules/local/squidpy/nhood_enrichment/main.nf @@ -2,7 +2,7 @@ process SQUIDPY_NHOOD_ENRICHMENT { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/squidpy/spatial_autocorr/main.nf b/modules/local/squidpy/spatial_autocorr/main.nf index 04bfc07a..f15f495b 100644 --- a/modules/local/squidpy/spatial_autocorr/main.nf +++ b/modules/local/squidpy/spatial_autocorr/main.nf @@ -2,7 +2,7 @@ process SQUIDPY_SPATIAL_AUTOCORR { tag "${meta.id}" label 'process_high' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/modules/local/squidpy/spatial_neighbors/main.nf b/modules/local/squidpy/spatial_neighbors/main.nf index b4da6f39..94e9df88 100644 --- a/modules/local/squidpy/spatial_neighbors/main.nf +++ b/modules/local/squidpy/spatial_neighbors/main.nf @@ -2,7 +2,7 @@ process SQUIDPY_SPATIAL_NEIGHBORS { tag "${meta.id}" label 'process_medium' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') diff --git a/nf-test.config b/nf-test.config index 4cb2cfef..47bbb7a3 100644 --- a/nf-test.config +++ b/nf-test.config @@ -34,6 +34,6 @@ config { // load the necessary plugins plugins { load "nft-utils@0.0.3" - load "nft-anndata@0.4.1" + load "nft-anndata@0.5.2" } } diff --git a/tests/helpers/duplicate_var_names.nf b/tests/helpers/duplicate_var_names.nf index 21e07335..2bdd589b 100644 --- a/tests/helpers/duplicate_var_names.nf +++ b/tests/helpers/duplicate_var_names.nf @@ -9,7 +9,7 @@ process DUPLICATE_VAR_NAMES { tag "${meta.id}" label 'process_single' - container "community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef" + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: tuple val(meta), path(h5ad, stageAs: "input.h5ad", arity: '1') From 1956dd5c3716c65691caa8546dac9a9824f475e5 Mon Sep 17 00:00:00 2001 From: Christophe Avenel Date: Sun, 11 Oct 2026 23:40:31 +0200 Subject: [PATCH 2/7] Raise resources for Visium HD-sized tables Several per-sample steps carry process_single (6 GB), sized for classic Visium. On Visium HD bins or segmented cells they are killed on the first attempt. Give them more memory through a config selector, alongside the existing one for the merged pre-processing steps. These steps are retried for memory rather than time, so cap their time limit too: escalating to 16 h makes retries hard to schedule. --- conf/modules.config | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 22ecf1a9..86ef1313 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -47,6 +47,16 @@ process { ] } + // Per-sample steps on Visium HD bins or cells need more than process_single + withName: 'SCANPY_FILTER|SCANPY_CALCULATE_QC_METRICS|SDATA_TO_LEGACY_ANNDATA|SDATA_UPDATE_TABLE|.*SPATIAL:SQUIDPY_.*' { + memory = { 36.GB * task.attempt } + } + + // Retried for memory rather than time; keep retries schedulable + withName: 'SCANPY_.*|SDATA_.*|SQUIDPY_.*|IMAGE_DOWNSCALE|MASK_TO_GEOJSON' { + time = { 4.h * task.attempt } + } + withName: FASTQC { publishDir = [ path: { "${params.outdir}/${meta.id}/fastqc" }, From 63b524ca7eaf32299e4d38d2fd2aed6e2383668b Mon Sep 17 00:00:00 2001 From: Christophe Avenel Date: Sun, 11 Oct 2026 23:40:31 +0200 Subject: [PATCH 3/7] Add cell segmentation modules and subworkflow - nf-core cellpose and stardist modules. The stardist module calls the StarDist API instead of stardist-predict2d, whose --n_tiles takes two values and so cannot tile RGB (YXC) images; untiled, a full-size H&E is killed for memory. Tile counts are derived from the image size. - IMAGE_DOWNSCALE: optional downscaling of the tissue image. - MASK_TO_GEOJSON: label mask to GeoJSON polygons in full-resolution pixels, classified as nucleus or cell. - SDATA_BIN_TO_CELL: group 2 um bins into cells with bin2cell, for processed Space Ranger output. - SEGMENTATION subworkflow tying the image steps together. --- modules.json | 11 + modules/local/image/downscale/main.nf | 28 +++ .../image/downscale/templates/downscale.py | 85 ++++++++ .../local/image/downscale/tests/main.nf.test | 33 +++ modules/local/sdata/bin_to_cell/main.nf | 29 +++ .../bin_to_cell/templates/bin_to_cell.py | 197 ++++++++++++++++++ .../sdata/bin_to_cell/tests/main.nf.test | 62 ++++++ .../segmentation/mask_to_geojson/main.nf | 29 +++ .../templates/mask_to_geojson.py | 99 +++++++++ .../mask_to_geojson/tests/main.nf.test | 34 +++ modules/nf-core/cellpose/environment.yml | 9 + modules/nf-core/cellpose/main.nf | 63 ++++++ modules/nf-core/cellpose/meta.yml | 158 ++++++++++++++ modules/nf-core/cellpose/tests/gpu.nf.test | 65 ++++++ .../nf-core/cellpose/tests/gpu.nf.test.snap | 129 ++++++++++++ modules/nf-core/cellpose/tests/main.nf.test | 65 ++++++ .../nf-core/cellpose/tests/main.nf.test.snap | 129 ++++++++++++ .../nf-core/cellpose/tests/nextflow.config | 9 + modules/nf-core/stardist/environment.yml | 26 +++ modules/nf-core/stardist/main.nf | 76 +++++++ modules/nf-core/stardist/meta.yml | 158 ++++++++++++++ modules/nf-core/stardist/stardist.diff | 108 ++++++++++ modules/nf-core/stardist/tests/gpu.nf.test | 61 ++++++ modules/nf-core/stardist/tests/main.nf.test | 59 ++++++ .../nf-core/stardist/tests/main.nf.test.snap | 168 +++++++++++++++ .../nf-core/stardist/tests/nextflow.config | 3 + subworkflows/local/segmentation/main.nf | 52 +++++ 27 files changed, 1945 insertions(+) create mode 100644 modules/local/image/downscale/main.nf create mode 100644 modules/local/image/downscale/templates/downscale.py create mode 100644 modules/local/image/downscale/tests/main.nf.test create mode 100644 modules/local/sdata/bin_to_cell/main.nf create mode 100644 modules/local/sdata/bin_to_cell/templates/bin_to_cell.py create mode 100644 modules/local/sdata/bin_to_cell/tests/main.nf.test create mode 100644 modules/local/segmentation/mask_to_geojson/main.nf create mode 100644 modules/local/segmentation/mask_to_geojson/templates/mask_to_geojson.py create mode 100644 modules/local/segmentation/mask_to_geojson/tests/main.nf.test create mode 100644 modules/nf-core/cellpose/environment.yml create mode 100644 modules/nf-core/cellpose/main.nf create mode 100644 modules/nf-core/cellpose/meta.yml create mode 100644 modules/nf-core/cellpose/tests/gpu.nf.test create mode 100644 modules/nf-core/cellpose/tests/gpu.nf.test.snap create mode 100644 modules/nf-core/cellpose/tests/main.nf.test create mode 100644 modules/nf-core/cellpose/tests/main.nf.test.snap create mode 100644 modules/nf-core/cellpose/tests/nextflow.config create mode 100644 modules/nf-core/stardist/environment.yml create mode 100644 modules/nf-core/stardist/main.nf create mode 100644 modules/nf-core/stardist/meta.yml create mode 100644 modules/nf-core/stardist/stardist.diff create mode 100644 modules/nf-core/stardist/tests/gpu.nf.test create mode 100644 modules/nf-core/stardist/tests/main.nf.test create mode 100644 modules/nf-core/stardist/tests/main.nf.test.snap create mode 100644 modules/nf-core/stardist/tests/nextflow.config create mode 100644 subworkflows/local/segmentation/main.nf diff --git a/modules.json b/modules.json index 9322af7f..847f5427 100644 --- a/modules.json +++ b/modules.json @@ -5,6 +5,11 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "cellpose": { + "branch": "master", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "installed_by": ["modules"] + }, "fastqc": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", @@ -26,6 +31,12 @@ "installed_by": ["modules"], "patch": "modules/nf-core/spaceranger/count/spaceranger-count.diff" }, + "stardist": { + "branch": "master", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "installed_by": ["modules"], + "patch": "modules/nf-core/stardist/stardist.diff" + }, "untar": { "branch": "master", "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", diff --git a/modules/local/image/downscale/main.nf b/modules/local/image/downscale/main.nf new file mode 100644 index 00000000..1939abe2 --- /dev/null +++ b/modules/local/image/downscale/main.nf @@ -0,0 +1,28 @@ +process IMAGE_DOWNSCALE { + tag "${meta.id}" + label 'process_high' + + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" + + input: + tuple val(meta), path(image) + val downscale + + output: + tuple val(meta), path("${prefix}_downscaled.tif"), emit: image + path "versions.yml" , emit: versions, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + template 'downscale.py' + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_downscaled.tif + touch versions.yml + """ +} diff --git a/modules/local/image/downscale/templates/downscale.py b/modules/local/image/downscale/templates/downscale.py new file mode 100644 index 00000000..970c2e10 --- /dev/null +++ b/modules/local/image/downscale/templates/downscale.py @@ -0,0 +1,85 @@ +#!/usr/bin/env python3 +""" +Downscale a full-resolution tissue image for segmentation. +""" + +# Disable OpenMP CPU topology detection for macOS compatibility +import os +os.environ["KMP_AFFINITY"] = "disabled" + +# Keep caches in the task's work directory, which is always writable and +# private to the task +os.environ["NUMBA_CACHE_DIR"] = os.path.join(os.getcwd(), ".cache", "numba") +os.environ["MPLCONFIGDIR"] = os.path.join(os.getcwd(), ".cache", "matplotlib") +os.environ["XDG_CACHE_HOME"] = os.path.join(os.getcwd(), ".cache") + +import importlib.metadata +import logging +import platform + +import cv2 +import numpy as np +import tifffile +import yaml + +logging.basicConfig(level=logging.INFO, format="%(name)s - %(levelname)s: %(message)s") +logger = logging.getLogger(__name__) + + +def to_rgb(img): + """Return an (H, W, 3) uint8-compatible array.""" + if img.ndim == 3 and img.shape[0] <= 4 and img.shape[0] < img.shape[2]: + img = np.moveaxis(img, 0, -1) + if img.ndim == 3 and img.shape[2] == 4: + img = img[..., :3] + if img.ndim == 2: + img = np.stack([img] * 3, axis=-1) + return img + + +def write_versions(process_name): + """Write software versions to a YAML file.""" + versions = { + process_name: { + "python": platform.python_version(), + "opencv": cv2.__version__, + "tifffile": importlib.metadata.version("tifffile"), + } + } + with open("versions.yml", "w") as f: + yaml.dump(versions, f) + + +def main(): + """Downscale the image by an integer factor.""" + + # Template variables + image = "${image}" + downscale = int("${downscale}") + output_image = "${prefix}_downscaled.tif" + process_name = "${task.process}" + + logger.info(f"Reading image: {image}") + if image.lower().endswith((".tif", ".tiff", ".btf")): + img = tifffile.imread(image) + else: + # JPEG or PNG: OpenCV reads colour images as BGR + img = cv2.imread(image, cv2.IMREAD_UNCHANGED) + if img is None: + raise ValueError(f"Could not read image: {image}") + if img.ndim == 3: + img = cv2.cvtColor(img, cv2.COLOR_BGRA2RGBA if img.shape[2] == 4 else cv2.COLOR_BGR2RGB) + img = to_rgb(img) + height, width = img.shape[:2] + logger.info(f"Image size: {width} x {height}, downscale factor: {downscale}") + + out = cv2.resize( + img, (width // downscale, height // downscale), interpolation=cv2.INTER_AREA + ) + tifffile.imwrite(output_image, out, compression="zlib") + logger.info(f"Written: {output_image} ({out.shape[1]} x {out.shape[0]})") + + write_versions(process_name) + +if __name__ == "__main__": + main() diff --git a/modules/local/image/downscale/tests/main.nf.test b/modules/local/image/downscale/tests/main.nf.test new file mode 100644 index 00000000..5863126d --- /dev/null +++ b/modules/local/image/downscale/tests/main.nf.test @@ -0,0 +1,33 @@ +nextflow_process { + + name "Test Process IMAGE_DOWNSCALE" + script "../main.nf" + process "IMAGE_DOWNSCALE" + + tag "modules" + tag "modules_local" + tag "image_downscale" + + test("homo_sapiens - tif - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2' ], file(params.pipelines_testdata_base_path + 'testdata/human-lung-cancer-post-xenium_hd_ffpe/Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_image.tif', checkIfExists: true) + ] + input[1] = 2 // downscale + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sdata/bin_to_cell/main.nf b/modules/local/sdata/bin_to_cell/main.nf new file mode 100644 index 00000000..dbd6f58f --- /dev/null +++ b/modules/local/sdata/bin_to_cell/main.nf @@ -0,0 +1,29 @@ +process SDATA_BIN_TO_CELL { + tag "${meta.id}" + label 'process_high' + + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" + + input: + tuple val(meta), path(sdata, stageAs: "input.zarr"), path(spaceranger_dir), path(segmentation) + val hd_bin_size + + output: + tuple val(meta), path("${prefix}.zarr"), emit: sdata + path "versions.yml" , emit: versions, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + template 'bin_to_cell.py' + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p ${prefix}.zarr + touch ${prefix}.zarr/.zgroup + touch versions.yml + """ +} diff --git a/modules/local/sdata/bin_to_cell/templates/bin_to_cell.py b/modules/local/sdata/bin_to_cell/templates/bin_to_cell.py new file mode 100644 index 00000000..30f1a8d9 --- /dev/null +++ b/modules/local/sdata/bin_to_cell/templates/bin_to_cell.py @@ -0,0 +1,197 @@ +#!/usr/bin/env python3 +""" +Group Visium HD 2 µm bins into cells with bin2cell, using a segmentation +(label mask or GeoJSON) in full-resolution image coordinates. The cell table +becomes the main table of the SpatialData object. +""" + +# Disable OpenMP CPU topology detection for macOS compatibility +import os +os.environ["KMP_AFFINITY"] = "disabled" + +# Keep caches in the task's work directory, which is always writable and +# private to the task +os.environ["NUMBA_CACHE_DIR"] = os.path.join(os.getcwd(), ".cache", "numba") +os.environ["MPLCONFIGDIR"] = os.path.join(os.getcwd(), ".cache", "matplotlib") +os.environ["XDG_CACHE_HOME"] = os.path.join(os.getcwd(), ".cache") + +import importlib.metadata +import json +import logging +import platform +import re + +import bin2cell as b2c +import numpy as np +import scanpy as sc +import shapely +import spatialdata +import tifffile +import yaml +from spatialdata.models import ShapesModel, TableModel +from spatialdata.transformations import get_transformation +from threadpoolctl import threadpool_limits + +logging.basicConfig(level=logging.INFO, format="%(name)s - %(levelname)s: %(message)s") +logger = logging.getLogger(__name__) + +# Limit BLAS/OpenMP threads to the allocated CPUs +threadpool_limits(int("${task.cpus}")) + +NO_CELLS_MESSAGE = ( + "No bins were assigned to a cell. The segmentation must cover the tissue " + "and be in full-resolution image pixel coordinates." +) + + +def is_geojson(segmentation): + """Return True if the segmentation file is GeoJSON rather than a mask.""" + return segmentation.lower().endswith((".geojson", ".json")) + + +def read_geojson_features(geojson_file): + """Return the features of a GeoJSON file.""" + with open(geojson_file) as f: + return json.load(f)["features"] + + +def labels_from_geojson(features, xy): + """Assign each bin centroid to the polygon containing it.""" + polygons = [shapely.geometry.shape(feat["geometry"]) for feat in features] + tree = shapely.STRtree(polygons) + bin_idx, poly_idx = tree.query(shapely.points(xy), predicate="within") + labels = np.zeros(len(xy), dtype=int) + labels[bin_idx] = poly_idx + 1 + return labels + + +def geojson_object_class(features): + """Return the classification name of the first feature, if any.""" + if not features: + return None + properties = features[0].get("properties") or {} + classification = properties.get("classification") or {} + return classification.get("name") + + +def labels_from_mask(mask_file, xy): + """Look up the label under each bin centroid.""" + if mask_file.endswith(".npy"): + mask = np.load(mask_file) + else: + mask = tifffile.imread(mask_file).squeeze() + rows = np.clip(xy[:, 1].astype(int), 0, mask.shape[0] - 1) + cols = np.clip(xy[:, 0].astype(int), 0, mask.shape[1] - 1) + return mask[rows, cols].astype(int) + + +def group_bins(spaceranger_dir, segmentation): + """Run bin2cell on the 2 µm bins and return a cell-level AnnData.""" + adata = b2c.read_visium(os.path.join(spaceranger_dir, "binned_outputs", "square_002um")) + adata.var_names_make_unique() + sc.pp.filter_cells(adata, min_counts=1) + + xy = np.asarray(adata.obsm["spatial"]) + object_class = None + if is_geojson(segmentation): + features = read_geojson_features(segmentation) + object_class = geojson_object_class(features) + labels = labels_from_geojson(features, xy) + else: + labels = labels_from_mask(segmentation, xy) + n_labelled = int((labels > 0).sum()) + logger.info(f"Bins with a label: {n_labelled} / {adata.n_obs}") + if n_labelled == 0: + raise ValueError(NO_CELLS_MESSAGE) + adata.obs["labels"] = labels + + # Nuclei are expanded into cells; whole-cell segmentations are not. As in + # Space Ranger, only a GeoJSON classified as "cell" is taken as whole + # cells; masks and unclassified GeoJSON are treated as nuclei. + whole_cells = object_class == "cell" + if whole_cells: + logger.info("Segmentation is whole cells: not expanding labels") + labels_key = "labels" + else: + logger.info("Segmentation is nuclei: expanding labels into cells") + b2c.expand_labels(adata, labels_key="labels", expanded_labels_key="labels_expanded") + labels_key = "labels_expanded" + cells = b2c.bin_to_cell(adata, labels_key=labels_key, spatial_keys=["spatial"]) + logger.info(f"Cells: {cells.n_obs}") + if cells.n_obs == 0: + raise ValueError(NO_CELLS_MESSAGE) + + library_id = list(adata.uns["spatial"].keys())[0] + mpp = adata.uns["spatial"][library_id]["scalefactors"]["microns_per_pixel"] + return cells, mpp + + +def add_cells_to_sdata(sdata, cells, mpp, sample_id, hd_bin_size): + """Add cells as circles and the cell table as the main table.""" + bins_name = f"{sample_id}_square_{hd_bin_size:03d}um" + cells_name = f"{sample_id}_cells" + table_name = f"{sample_id}_table" + + # Circle radius from the number of 2 µm bins per cell + radius = np.sqrt(cells.obs["bin_count"].to_numpy() * 4 / np.pi) / mpp + sdata.shapes[cells_name] = ShapesModel.parse( + np.asarray(cells.obsm["spatial"]), + geometry=0, + radius=radius, + index=cells.obs_names.astype(int), + transformations=get_transformation(sdata.shapes[bins_name], get_all=True), + ) + + cells.obs["cell_id"] = cells.obs_names.astype(int) + cells.obs["region"] = cells_name + cells.obs["region"] = cells.obs["region"].astype("category") + # bin2cell copies the images into uns; SpatialData already holds them + cells.uns.pop("spatial", None) + + sdata.tables[f"{sample_id}_bin_table"] = sdata.tables[table_name] + del sdata.tables[table_name] + sdata.tables[table_name] = TableModel.parse( + cells, region=cells_name, region_key="region", instance_key="cell_id" + ) + + +def write_versions(process_name): + """Write software versions to a YAML file.""" + versions = { + process_name: { + "python": platform.python_version(), + "bin2cell": importlib.metadata.version("bin2cell"), + "spatialdata": importlib.metadata.version("spatialdata"), + } + } + with open("versions.yml", "w") as f: + yaml.dump(versions, f) + + +def main(): + """Group bins into cells and update the SpatialData object.""" + + # Template variables + input_sdata = "${sdata}" + spaceranger_dir = "${spaceranger_dir}" + segmentation = "${segmentation}" + hd_bin_size = int("${hd_bin_size}") + sample_id = "${meta.id}" + output_sdata = "${prefix}.zarr" + process_name = "${task.process}" + + # Sample ID must only contain alphanumerics, underscores and dashes + sample_id = re.sub(r"[^a-zA-Z0-9_-]", "", sample_id) + + cells, mpp = group_bins(spaceranger_dir, segmentation) + + sdata = spatialdata.read_zarr(input_sdata) + add_cells_to_sdata(sdata, cells, mpp, sample_id, hd_bin_size) + + logger.info(f"Writing SpatialData to: {output_sdata}") + sdata.write(output_sdata, overwrite=True) + + write_versions(process_name) + +if __name__ == "__main__": + main() diff --git a/modules/local/sdata/bin_to_cell/tests/main.nf.test b/modules/local/sdata/bin_to_cell/tests/main.nf.test new file mode 100644 index 00000000..a521d81a --- /dev/null +++ b/modules/local/sdata/bin_to_cell/tests/main.nf.test @@ -0,0 +1,62 @@ +nextflow_process { + + name "Test Process SDATA_BIN_TO_CELL" + script "../main.nf" + process "SDATA_BIN_TO_CELL" + + tag "modules" + tag "modules_local" + tag "sdata_bin_to_cell" + + // N.B. + // There is no Visium HD Space Ranger output small enough for + // nf-core/test-datasets, so only a stub test is possible. + + test("homo_sapiens - zarr - stub") { + + options "-stub" + + setup { + run("UNTAR") { + script "../../../../nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ id: 'CytAssist_11mm_FFPE_Human_Glioblastoma_2' ], file(params.pipelines_testdata_base_path + 'testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs.tar.gz', checkIfExists: true) + ] + """ + } + } + run("SDATA_READ_VISIUM") { + script "../../read_visium/main.nf" + process { + """ + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size + """ + } + } + } + + when { + process { + """ + input[0] = SDATA_READ_VISIUM.out.sdata + .join(UNTAR.out.untar) + .map { meta, sdata, outs -> [ + meta, sdata, outs, + file(params.pipelines_testdata_base_path + 'testdata/human-lung-cancer-post-xenium_hd_ffpe/Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_image.tif', checkIfExists: true) + ] } + input[1] = 8 // hd_bin_size + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/segmentation/mask_to_geojson/main.nf b/modules/local/segmentation/mask_to_geojson/main.nf new file mode 100644 index 00000000..5d3251ec --- /dev/null +++ b/modules/local/segmentation/mask_to_geojson/main.nf @@ -0,0 +1,29 @@ +process MASK_TO_GEOJSON { + tag "${meta.id}" + label 'process_medium' + + container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" + + input: + tuple val(meta), path(mask) + val downscale + val object_class + + output: + tuple val(meta), path("${prefix}_segmentation.geojson"), emit: geojson + path "versions.yml" , emit: versions, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + template 'mask_to_geojson.py' + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_segmentation.geojson + touch versions.yml + """ +} diff --git a/modules/local/segmentation/mask_to_geojson/templates/mask_to_geojson.py b/modules/local/segmentation/mask_to_geojson/templates/mask_to_geojson.py new file mode 100644 index 00000000..100dc592 --- /dev/null +++ b/modules/local/segmentation/mask_to_geojson/templates/mask_to_geojson.py @@ -0,0 +1,99 @@ +#!/usr/bin/env python3 +""" +Convert a label mask to GeoJSON polygons in full-resolution pixel coordinates. +The output follows the Space Ranger segmentation GeoJSON format. +""" + +# Disable OpenMP CPU topology detection for macOS compatibility +import os +os.environ["KMP_AFFINITY"] = "disabled" + +# Keep caches in the task's work directory, which is always writable and +# private to the task +os.environ["NUMBA_CACHE_DIR"] = os.path.join(os.getcwd(), ".cache", "numba") +os.environ["MPLCONFIGDIR"] = os.path.join(os.getcwd(), ".cache", "matplotlib") +os.environ["XDG_CACHE_HOME"] = os.path.join(os.getcwd(), ".cache") + +import importlib.metadata +import json +import logging +import platform + +import cv2 +import numpy as np +import tifffile +import yaml +from skimage.measure import regionprops + +logging.basicConfig(level=logging.INFO, format="%(name)s - %(levelname)s: %(message)s") +logger = logging.getLogger(__name__) + + +def label_to_polygon(mask, prop, scale): + """Return the outer contour of one label as a closed coordinate list.""" + min_row, min_col, max_row, max_col = prop.bbox + binary = (mask[min_row:max_row, min_col:max_col] == prop.label).astype(np.uint8) + contours, _ = cv2.findContours(binary, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE) + contour = max(contours, key=cv2.contourArea).reshape(-1, 2) + if len(contour) < 3: + return None + # Contour points are pixel indices; map pixel centres back to full + # resolution (identity when scale is 1) + coords = (contour + [min_col, min_row] + 0.5) * scale - 0.5 + coords = coords.tolist() + coords.append(coords[0]) + return coords + + +def write_versions(process_name): + """Write software versions to a YAML file.""" + versions = { + process_name: { + "python": platform.python_version(), + "opencv": cv2.__version__, + "scikit-image": importlib.metadata.version("scikit-image"), + } + } + with open("versions.yml", "w") as f: + yaml.dump(versions, f) + + +def main(): + """Convert mask to GeoJSON.""" + + # Template variables + mask_file = "${mask}" + # Factor the image was shrunk by before segmentation; polygons are scaled back up + scale = float("${downscale}") + object_class = "${object_class}" + output_geojson = "${prefix}_segmentation.geojson" + process_name = "${task.process}" + + logger.info(f"Reading mask: {mask_file}") + mask = tifffile.imread(mask_file) + if mask.ndim > 2: + mask = mask.squeeze() + + features = [] + for prop in regionprops(mask): + coords = label_to_polygon(mask, prop, scale) + if coords is None: + continue + features.append({ + "type": "Feature", + "geometry": {"type": "Polygon", "coordinates": [coords]}, + "properties": { + "cell_id": int(prop.label), + "classification": {"name": object_class}, + }, + }) + logger.info(f"Polygons: {len(features)}") + + with open(output_geojson, "w") as f: + json.dump({"type": "FeatureCollection", "features": features}, f) + logger.info(f"Written: {output_geojson}") + + write_versions(process_name) + +if __name__ == "__main__": + main() diff --git a/modules/local/segmentation/mask_to_geojson/tests/main.nf.test b/modules/local/segmentation/mask_to_geojson/tests/main.nf.test new file mode 100644 index 00000000..3b403ef2 --- /dev/null +++ b/modules/local/segmentation/mask_to_geojson/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process MASK_TO_GEOJSON" + script "../main.nf" + process "MASK_TO_GEOJSON" + + tag "modules" + tag "modules_local" + tag "mask_to_geojson" + + test("homo_sapiens - tif - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2' ], file(params.pipelines_testdata_base_path + 'testdata/human-lung-cancer-post-xenium_hd_ffpe/Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_image.tif', checkIfExists: true) + ] + input[1] = 2 // scale + input[2] = 'nucleus' // object_class + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/cellpose/environment.yml b/modules/nf-core/cellpose/environment.yml new file mode 100644 index 00000000..e22d2601 --- /dev/null +++ b/modules/nf-core/cellpose/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::python=3.12.12 + - pip: + - cellpose==4.0.9 diff --git a/modules/nf-core/cellpose/main.nf b/modules/nf-core/cellpose/main.nf new file mode 100644 index 00000000..571a1b3a --- /dev/null +++ b/modules/nf-core/cellpose/main.nf @@ -0,0 +1,63 @@ +process CELLPOSE { + tag "${meta.id}" + label 'process_medium' + label 'process_gpu' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb670191b7ae1a9fd5449746453916c7014b9ea622942ca76a7cb40da7deee46/data' : + 'community.wave.seqera.io/library/python_pip_cellpose:fdf7a8c3a305a26e' }" + + input: + tuple val(meta), path(image) + path(model) + + output: + tuple val(meta), path("${prefix}/*masks.tif"), emit: mask + tuple val(meta), path("${prefix}/*flows.tif"), emit: flows, optional: true + tuple val(meta), path("${prefix}/*seg.npy"), emit: cells, optional: true + tuple val("${task.process}"), val('cellpose'), eval("cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'"), topic: versions, emit: versions_cellpose + tuple val("${task.process}"), val('python'), eval("cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'"), topic: versions, emit: versions_python + tuple val("${task.process}"), val('torch'), eval("cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'"), topic: versions, emit: versions_torch + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def model_command = model ? "--pretrained_model ${model}" : "" + def gpu_flag = task.accelerator ? "--use_gpu" : "" + prefix = task.ext.prefix ?: "${meta.id}" + """ + export OMP_NUM_THREADS=${task.cpus} + export MKL_NUM_THREADS=${task.cpus} + # Container runs as root with HOME=/ which is not writable + export HOME=\$PWD + export MPLCONFIGDIR=\$PWD/.matplotlib + export CELLPOSE_LOCAL_MODELS_PATH=\$PWD/.cellpose + mkdir -p \$MPLCONFIGDIR \$CELLPOSE_LOCAL_MODELS_PATH + + cellpose \\ + --image_path ${image} \\ + --save_tif \\ + --verbose \\ + ${gpu_flag} \\ + ${model_command} \\ + ${args} + + mkdir -p ${prefix} + mv *masks.tif ${prefix}/ + mv *flows.tif ${prefix}/ 2>/dev/null || true + mv *seg.npy ${prefix}/ 2>/dev/null || true + """ + + stub: + def name = image.name + def base = name.lastIndexOf('.') != -1 ? name[0..name.lastIndexOf('.') - 1] : name + prefix = task.ext.prefix ?: "${meta.id}" + + """ + mkdir -p ${prefix} + touch ${prefix}/${base}_cp_masks.tif + """ +} diff --git a/modules/nf-core/cellpose/meta.yml b/modules/nf-core/cellpose/meta.yml new file mode 100644 index 00000000..cb7a89a7 --- /dev/null +++ b/modules/nf-core/cellpose/meta.yml @@ -0,0 +1,158 @@ +name: "cellpose" +description: cellpose segments cells in images using GPU-accelerated deep learning +keywords: + - segmentation + - image + - cellpose + - gpu + - spatial-transcriptomics +tools: + - "cellpose": + description: "cellpose is an anatomical segmentation algorithm written in Python + 3 by Carsen Stringer and Marius Pachitariu" + homepage: "https://github.com/MouseLand/cellpose" + documentation: "https://cellpose.readthedocs.io/en/latest/command.html" + tool_dev_url: "https://github.com/MouseLand/cellpose" + doi: 10.1038/s41592-022-01663-4 + licence: ["BSD 3-Clause"] + identifier: biotools:cellpose +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + (sample id) + - image: + type: file + description: tif file ready for segmentation + pattern: "*.{tif,tiff}" + ontologies: [] + - model: + type: file + description: | + Optional custom cellpose model file. When provided, passed as + --pretrained_model to cellpose. Pass [] (empty list) to use the + default model (cpsam in cellpose 4). + pattern: "*" + ontologies: [] +output: + mask: + - - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "${prefix}/*masks.tif": + type: file + description: labelled mask output from cellpose in tif format + pattern: "${prefix}/*masks.tif" + ontologies: [] + flows: + - - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "${prefix}/*flows.tif": + type: file + description: cell flow output from cellpose + pattern: "${prefix}/*flows.tif" + ontologies: [] + cells: + - - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "${prefix}/*seg.npy": + type: file + description: numpy array with cell segmentation data + pattern: "${prefix}/*seg.npy" + ontologies: [] + versions_cellpose: + - - ${task.process}: + type: string + description: The name of the process + - cellpose: + type: string + description: The name of the tool + - "cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'": + type: eval + description: The expression to obtain the version of the tool + versions_python: + - - ${task.process}: + type: string + description: The name of the process + - python: + type: string + description: The name of the tool + - "cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'": + type: eval + description: The expression to obtain the version of the tool + versions_torch: + - - ${task.process}: + type: string + description: The name of the process + - torch: + type: string + description: The name of the tool + - "cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - cellpose: + type: string + description: The name of the tool + - "cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'": + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - python: + type: string + description: The name of the tool + - "cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'": + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - torch: + type: string + description: The name of the tool + - "cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'": + type: eval + description: The expression to obtain the version of the tool +notes: | + When `accelerator` is set (e.g. `accelerator = 1`), the module + automatically passes `--use_gpu` to cellpose. The container (built via Seqera + Containers) includes PyTorch 2.10.0 with CUDA 12.8 and falls back to CPU + automatically when no GPU is available. Use the `process_gpu` label to request + GPU resources from your executor. When running with conda/mamba, GPU support + depends on having a CUDA-enabled PyTorch installation in your environment. + + Model selection via the model input channel: + - Custom model file: file("/path/to/model") + - Default (cpsam): [] + + Additional cellpose CLI arguments can be passed via `task.ext.args`: + ext.args = '--diameter 30 --flow_threshold 0.4 --cellprob_threshold 0' + + Deprecated in cellpose 4.0.1+: `--chan`, `--chan2`, `--invert`, `--all_channels`, + `--diam_mean`, `--pretrained_model_ortho`. Do not pass these via ext.args. + + Model weights are not bundled in the container. Cellpose downloads them on first + use to `$CELLPOSE_LOCAL_MODELS_PATH` (set to the work directory). +authors: + - "@josenimo" + - "@FloWuenne" + - "@dongzehe" +maintainers: + - "@josenimo" + - "@FloWuenne" + - "@kbestak" diff --git a/modules/nf-core/cellpose/tests/gpu.nf.test b/modules/nf-core/cellpose/tests/gpu.nf.test new file mode 100644 index 00000000..5ed2fe81 --- /dev/null +++ b/modules/nf-core/cellpose/tests/gpu.nf.test @@ -0,0 +1,65 @@ +nextflow_process { + + name "Test Process CELLPOSE on GPU" + script "../main.nf" + process "CELLPOSE" + + tag "modules" + tag "modules_nfcore" + tag "cellpose" + tag "gpu" + + test("cellpose - gpu - with flows, no model") { + + when { + config "./nextflow.config" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + def mask_files = process.out.mask[0][1].collect { file(it) } + assertAll ( + { assert process.success }, + { assert mask_files.size() == 3 }, + { assert snapshot(mask_files.collect { it.name }).match("mask_files") }, + { assert mask_files.every { it.size() > 0 } }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("versions") } + ) + } + + } + + test("cellpose - gpu - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/cellpose/tests/gpu.nf.test.snap b/modules/nf-core/cellpose/tests/gpu.nf.test.snap new file mode 100644 index 00000000..f4540356 --- /dev/null +++ b/modules/nf-core/cellpose/tests/gpu.nf.test.snap @@ -0,0 +1,129 @@ +{ + "cellpose - gpu - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "cycif_tonsil_registered.ome_cp_masks.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "CELLPOSE", + "cellpose", + "4.0.9" + ] + ], + "4": [ + [ + "CELLPOSE", + "python", + "3.12.12" + ] + ], + "5": [ + [ + "CELLPOSE", + "torch", + "2.10.0" + ] + ], + "cells": [ + + ], + "flows": [ + + ], + "mask": [ + [ + { + "id": "test" + }, + "cycif_tonsil_registered.ome_cp_masks.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_cellpose": [ + [ + "CELLPOSE", + "cellpose", + "4.0.9" + ] + ], + "versions_python": [ + [ + "CELLPOSE", + "python", + "3.12.12" + ] + ], + "versions_torch": [ + [ + "CELLPOSE", + "torch", + "2.10.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-09T15:04:09.037710153" + }, + "mask_files": { + "content": [ + [ + "cycif_tonsil_registered.ome_cp_masks.tif", + "cycif_tonsil_registered.ome_dP_cp_masks.tif", + "cycif_tonsil_registered.ome_flows_cp_masks.tif" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-09T15:04:01.076800875" + }, + "versions": { + "content": [ + { + "versions_cellpose": [ + [ + "CELLPOSE", + "cellpose", + "4.0.9" + ] + ], + "versions_python": [ + [ + "CELLPOSE", + "python", + "3.12.12" + ] + ], + "versions_torch": [ + [ + "CELLPOSE", + "torch", + "2.10.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-09T15:04:01.110561727" + } +} \ No newline at end of file diff --git a/modules/nf-core/cellpose/tests/main.nf.test b/modules/nf-core/cellpose/tests/main.nf.test new file mode 100644 index 00000000..552de09b --- /dev/null +++ b/modules/nf-core/cellpose/tests/main.nf.test @@ -0,0 +1,65 @@ +nextflow_process { + + name "Test Process CELLPOSE" + script "../main.nf" + process "CELLPOSE" + + tag "modules" + tag "modules_nfcore" + tag "cellpose" + + test("cellpose - with flows, no model") { + + when { + config "./nextflow.config" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + def mask_files = process.out.mask[0][1].collect { file(it) } + assertAll ( + { assert process.success }, + { assert mask_files.size() == 3 }, + { assert snapshot(mask_files.collect { it.name }).match("mask_files") }, + { assert mask_files.every { it.size() > 0 } }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("versions") } + ) + } + + } + + + test("cellpose - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/cellpose/tests/main.nf.test.snap b/modules/nf-core/cellpose/tests/main.nf.test.snap new file mode 100644 index 00000000..e0bb7b8d --- /dev/null +++ b/modules/nf-core/cellpose/tests/main.nf.test.snap @@ -0,0 +1,129 @@ +{ + "mask_files": { + "content": [ + [ + "cycif_tonsil_registered.ome_cp_masks.tif", + "cycif_tonsil_registered.ome_dP_cp_masks.tif", + "cycif_tonsil_registered.ome_flows_cp_masks.tif" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-06T17:10:18.771259168" + }, + "versions": { + "content": [ + { + "versions_cellpose": [ + [ + "CELLPOSE", + "cellpose", + "4.0.9" + ] + ], + "versions_python": [ + [ + "CELLPOSE", + "python", + "3.12.12" + ] + ], + "versions_torch": [ + [ + "CELLPOSE", + "torch", + "2.10.0+cu128" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-09T17:04:23.355608629" + }, + "cellpose - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "cycif_tonsil_registered.ome_cp_masks.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "CELLPOSE", + "cellpose", + "4.0.9" + ] + ], + "4": [ + [ + "CELLPOSE", + "python", + "3.12.12" + ] + ], + "5": [ + [ + "CELLPOSE", + "torch", + "2.10.0+cu128" + ] + ], + "cells": [ + + ], + "flows": [ + + ], + "mask": [ + [ + { + "id": "test" + }, + "cycif_tonsil_registered.ome_cp_masks.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_cellpose": [ + [ + "CELLPOSE", + "cellpose", + "4.0.9" + ] + ], + "versions_python": [ + [ + "CELLPOSE", + "python", + "3.12.12" + ] + ], + "versions_torch": [ + [ + "CELLPOSE", + "torch", + "2.10.0+cu128" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-09T17:04:40.207673084" + } +} \ No newline at end of file diff --git a/modules/nf-core/cellpose/tests/nextflow.config b/modules/nf-core/cellpose/tests/nextflow.config new file mode 100644 index 00000000..986cb405 --- /dev/null +++ b/modules/nf-core/cellpose/tests/nextflow.config @@ -0,0 +1,9 @@ +docker { + fixOwnership = true +} + +process { + withName: "CELLPOSE" { + ext.args = '--no_npy --save_flows' + } +} diff --git a/modules/nf-core/stardist/environment.yml b/modules/nf-core/stardist/environment.yml new file mode 100644 index 00000000..ddba86ea --- /dev/null +++ b/modules/nf-core/stardist/environment.yml @@ -0,0 +1,26 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::python=3.12.12 + - pip: + - stardist==0.9.2 + - tifffile==2026.3.3 + - imagecodecs==2026.1.14 + # For conda GPU support, use tensorflow[and-cuda]==2.20.0 instead + # The followings are needed in seqera containers UI + - tensorflow==2.20.0 + - nvidia-cublas-cu12==12.9.1.4 + - nvidia-cuda-cupti-cu12==12.9.79 + - nvidia-cuda-nvcc-cu12==12.9.86 + - nvidia-cuda-nvrtc-cu12==12.9.86 + - nvidia-cuda-runtime-cu12==12.9.79 + - nvidia-cudnn-cu12==9.19.0.56 + - nvidia-cufft-cu12==11.4.1.4 + - nvidia-curand-cu12==10.3.10.19 + - nvidia-cusolver-cu12==11.7.5.82 + - nvidia-cusparse-cu12==12.5.10.65 + - nvidia-nccl-cu12==2.29.7 + - nvidia-nvjitlink-cu12==12.9.86 diff --git a/modules/nf-core/stardist/main.nf b/modules/nf-core/stardist/main.nf new file mode 100644 index 00000000..76b3454d --- /dev/null +++ b/modules/nf-core/stardist/main.nf @@ -0,0 +1,76 @@ +process STARDIST { + tag "$meta.id" + label 'process_medium' + label 'process_gpu' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d964e0bef867bb2ff1a309c9c087d8d83ac734ce3aa315dd8311d4c1bfdafd8e/data' : + 'community.wave.seqera.io/library/python_pip_imagecodecs_nvidia-cublas-cu12_pruned:b668bcb6d531d350' }" + + input: + tuple val(meta), path(image) + tuple val(model_name), path(model_path) + + output: + tuple val(meta), path("*.stardist.tif"), emit: mask + tuple val("${task.process}"), val('stardist'), eval("pip show stardist | sed -n 's/^Version: //p'"), topic: versions, emit: versions_stardist + tuple val("${task.process}"), val('python'), eval("python --version | sed 's/Python //'"), topic: versions, emit: versions_python + tuple val("${task.process}"), val('tensorflow'), eval("pip show tensorflow | sed -n 's/^Version: //p'"), topic: versions, emit: versions_tensorflow + tuple val("${task.process}"), val('tifffile'), eval("pip show tifffile | sed -n 's/^Version: //p'"), topic: versions, emit: versions_tifffile + + when: + task.ext.when == null || task.ext.when + + // The `stardist-predict2d` script declares `--n_tiles` with `nargs=2`, so it + // cannot tile RGB input, which needs one tile count per axis. Untiled, a + // full-size H&E allocates its ray array whole and is OOM-killed. + script: + // Extra keyword arguments to `predict_instances`, e.g. 'prob_thresh=0.6, nms_thresh=0.3' + def args = task.ext.args ? ", ${task.ext.args}" : '' + def prefix = task.ext.prefix ?: "${meta.id}" + def model_ref = model_path ? "${model_path}" : "${model_name}" + """ + python <<'PY' + import logging + import pathlib + + import numpy as np + from csbdeep.utils import normalize + from imageio import imread + from stardist.models import StarDist2D + from tifffile import imwrite + + logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s") + logger = logging.getLogger(__name__) + + img = imread("${image}") + if img.ndim not in (2, 3): + raise ValueError("only 2d and 3d images are supported, got %dd" % img.ndim) + + # Roughly 2000 px per tile + n_tiles = max(1, int(np.ceil(max(img.shape[:2]) / 2000))) + # One tile count per axis; never tile the channel axis of YXC input. + tiles = (n_tiles, n_tiles) if img.ndim == 2 else (n_tiles, n_tiles, 1) + logger.info(f"Image {img.shape[1]} x {img.shape[0]}, n_tiles={tiles}") + + model_ref = "${model_ref}" + if pathlib.Path(model_ref).is_dir(): + model = StarDist2D(None, name=model_ref) + else: + model = StarDist2D.from_pretrained(model_ref) + if model is None: + raise ValueError("unknown model: %s" % model_ref) + + img = normalize(img, 1, 99.8) + labels, _ = model.predict_instances(img, n_tiles=tiles${args}) + imwrite("${prefix}.stardist.tif", labels, compression="zlib") + PY + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.stardist.tif + """ +} diff --git a/modules/nf-core/stardist/meta.yml b/modules/nf-core/stardist/meta.yml new file mode 100644 index 00000000..4a27a6bf --- /dev/null +++ b/modules/nf-core/stardist/meta.yml @@ -0,0 +1,158 @@ +name: "stardist" +description: Cell and nuclear segmentation with star-convex shapes +keywords: + - stardist + - segmentation + - image + - gpu + - spatial-transcriptomics +tools: + - "stardist": + description: "Stardist is an cell segmentation tool developed in Python by Martin + Weigert and Uwe Schmidt" + homepage: "https://stardist.net/" + documentation: "https://stardist.net/faq/" + tool_dev_url: "https://github.com/stardist/stardist" + doi: "10.1109/ISBIC56247.2022.9854534" + licence: + - "BSD 3-Clause" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - image: + type: file + description: Single-channel (YX) or RGB (YXC, e.g. H&E) image + pattern: "*.{tiff,tif}" + ontologies: [] + - - model_name: + type: string + description: | + Name of a pretrained StarDist model (e.g. '2D_versatile_fluo', + '2D_versatile_he'). Used when model_path is not provided. + Pass '' (empty string) if providing a custom model path. + - model_path: + type: file + description: | + Optional path to a custom StarDist model directory. When provided, + takes precedence over model_name. Pass [] (empty list) to use a + pretrained model name instead. + pattern: "*" + ontologies: [] +output: + mask: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.stardist.tif": + type: file + description: labelled mask output from stardist in tif format. + pattern: "*.{tiff,tif}" + ontologies: [] + versions_stardist: + - - ${task.process}: + type: string + description: The name of the process + - stardist: + type: string + description: The name of the tool + - "pip show stardist | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool + versions_python: + - - ${task.process}: + type: string + description: The name of the process + - python: + type: string + description: The name of the tool + - python --version | sed 's/Python //': + type: eval + description: The expression to obtain the version of the tool + versions_tensorflow: + - - ${task.process}: + type: string + description: The name of the process + - tensorflow: + type: string + description: The name of the tool + - "pip show tensorflow | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool + versions_tifffile: + - - ${task.process}: + type: string + description: The name of the process + - tifffile: + type: string + description: The name of the tool + - "pip show tifffile | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - stardist: + type: string + description: The name of the tool + - "pip show stardist | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - python: + type: string + description: The name of the tool + - python --version | sed 's/Python //': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - tensorflow: + type: string + description: The name of the tool + - "pip show tensorflow | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - tifffile: + type: string + description: The name of the tool + - "pip show tifffile | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool +authors: + - "@migueLib" + - "@dongzehe" +maintainers: + - "@migueLib" +notes: | + GPU support: The container (built via Seqera Containers) includes TensorFlow 2.20.0 + with CUDA support and falls back to CPU automatically when no GPU is available. + Use the `process_gpu` label to request GPU resources from your executor. + When running with conda/mamba, GPU support depends on having a CUDA-enabled + TensorFlow installation in your environment. + + Model selection via the model input channel [model_name, model_path]: + - Pretrained model: [ '2D_versatile_fluo', [] ] + - Custom model directory: [ '', file("/path/to/model") ] + + The image is normalised to the 1-99.8 percentile range and predicted in tiles + of roughly 2000 px per side (the channel axis of RGB input is never tiled). + `task.ext.args` is passed as extra keyword arguments to + `StarDist2D.predict_instances`, for example: + ext.args = 'prob_thresh=0.6, nms_thresh=0.3' + + Model weights are not bundled in the container. StarDist downloads pretrained + models on first use to ~/.keras/models/. diff --git a/modules/nf-core/stardist/stardist.diff b/modules/nf-core/stardist/stardist.diff new file mode 100644 index 00000000..031569c5 --- /dev/null +++ b/modules/nf-core/stardist/stardist.diff @@ -0,0 +1,108 @@ +Changes in component 'nf-core/stardist' +Changes in 'stardist/main.nf': +--- modules/nf-core/stardist/main.nf ++++ modules/nf-core/stardist/main.nf +@@ -22,15 +22,50 @@ + when: + task.ext.when == null || task.ext.when + ++ // The `stardist-predict2d` script declares `--n_tiles` with `nargs=2`, so it ++ // cannot tile RGB input, which needs one tile count per axis. Untiled, a ++ // full-size H&E allocates its ray array whole and is OOM-killed. + script: +- def args = task.ext.args ?: '' +- def model_command = model_path ? "-m ${model_path}" : model_name ? "-m ${model_name}" : "" ++ // Extra keyword arguments to `predict_instances`, e.g. 'prob_thresh=0.6, nms_thresh=0.3' ++ def args = task.ext.args ? ", ${task.ext.args}" : '' ++ def prefix = task.ext.prefix ?: "${meta.id}" ++ def model_ref = model_path ? "${model_path}" : "${model_name}" + """ +- stardist-predict2d \\ +- -i $image \\ +- -o . \\ +- $model_command \\ +- $args ++ python <<'PY' ++ import logging ++ import pathlib ++ ++ import numpy as np ++ from csbdeep.utils import normalize ++ from imageio import imread ++ from stardist.models import StarDist2D ++ from tifffile import imwrite ++ ++ logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s") ++ logger = logging.getLogger(__name__) ++ ++ img = imread("${image}") ++ if img.ndim not in (2, 3): ++ raise ValueError("only 2d and 3d images are supported, got %dd" % img.ndim) ++ ++ # Roughly 2000 px per tile ++ n_tiles = max(1, int(np.ceil(max(img.shape[:2]) / 2000))) ++ # One tile count per axis; never tile the channel axis of YXC input. ++ tiles = (n_tiles, n_tiles) if img.ndim == 2 else (n_tiles, n_tiles, 1) ++ logger.info(f"Image {img.shape[1]} x {img.shape[0]}, n_tiles={tiles}") ++ ++ model_ref = "${model_ref}" ++ if pathlib.Path(model_ref).is_dir(): ++ model = StarDist2D(None, name=model_ref) ++ else: ++ model = StarDist2D.from_pretrained(model_ref) ++ if model is None: ++ raise ValueError("unknown model: %s" % model_ref) ++ ++ img = normalize(img, 1, 99.8) ++ labels, _ = model.predict_instances(img, n_tiles=tiles${args}) ++ imwrite("${prefix}.stardist.tif", labels, compression="zlib") ++ PY + """ + + stub: + +Changes in 'stardist/meta.yml': +--- modules/nf-core/stardist/meta.yml ++++ modules/nf-core/stardist/meta.yml +@@ -25,7 +25,7 @@ + e.g. `[ id:'sample1' ]` + - image: + type: file +- description: Single channel nuclear image ++ description: Single-channel (YX) or RGB (YXC, e.g. H&E) image + pattern: "*.{tiff,tif}" + ontologies: [] + - - model_name: +@@ -33,8 +33,7 @@ + description: | + Name of a pretrained StarDist model (e.g. '2D_versatile_fluo', + '2D_versatile_he'). Used when model_path is not provided. +- Pass '' (empty string) if providing a custom model path or +- passing -m via ext.args. ++ Pass '' (empty string) if providing a custom model path. + - model_path: + type: file + description: | +@@ -148,10 +147,12 @@ + Model selection via the model input channel [model_name, model_path]: + - Pretrained model: [ '2D_versatile_fluo', [] ] + - Custom model directory: [ '', file("/path/to/model") ] +- - Via ext.args only: [ '', [] ] (then set ext.args = '-m ...') + +- Additional stardist CLI arguments can be passed via `task.ext.args`: +- ext.args = '--n_tiles 4,4 --prob_thresh 0.5 --nms_thresh 0.3' ++ The image is normalised to the 1-99.8 percentile range and predicted in tiles ++ of roughly 2000 px per side (the channel axis of RGB input is never tiled). ++ `task.ext.args` is passed as extra keyword arguments to ++ `StarDist2D.predict_instances`, for example: ++ ext.args = 'prob_thresh=0.6, nms_thresh=0.3' + + Model weights are not bundled in the container. StarDist downloads pretrained + models on first use to ~/.keras/models/. + +'modules/nf-core/stardist/environment.yml' is unchanged +'modules/nf-core/stardist/tests/gpu.nf.test' is unchanged +'modules/nf-core/stardist/tests/main.nf.test' is unchanged +'modules/nf-core/stardist/tests/main.nf.test.snap' is unchanged +'modules/nf-core/stardist/tests/nextflow.config' is unchanged +************************************************************ diff --git a/modules/nf-core/stardist/tests/gpu.nf.test b/modules/nf-core/stardist/tests/gpu.nf.test new file mode 100644 index 00000000..11c72ba8 --- /dev/null +++ b/modules/nf-core/stardist/tests/gpu.nf.test @@ -0,0 +1,61 @@ +nextflow_process { + + name "Test Process STARDIST on GPU" + script "../main.nf" + process "STARDIST" + + tag "modules" + tag "modules_nfcore" + tag "stardist" + tag "gpu" + + test("stardist2d - gpu - tif") { + + when { + config "./nextflow.config" + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true) + ] + input[1] = [ '2D_versatile_fluo', [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("stardist2d - gpu - tif - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true) + ] + input[1] = [ '2D_versatile_fluo', [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/stardist/tests/main.nf.test b/modules/nf-core/stardist/tests/main.nf.test new file mode 100644 index 00000000..5b3e2089 --- /dev/null +++ b/modules/nf-core/stardist/tests/main.nf.test @@ -0,0 +1,59 @@ +nextflow_process { + name "Test Process STARDIST" + script "../main.nf" + process "STARDIST" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "stardist" + + test("stardist2d - tif") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true) + ] + input[1] = [ '2D_versatile_fluo', [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("stardist2d - tif - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true) + ] + input[1] = [ '2D_versatile_fluo', [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/stardist/tests/main.nf.test.snap b/modules/nf-core/stardist/tests/main.nf.test.snap new file mode 100644 index 00000000..cdc2996c --- /dev/null +++ b/modules/nf-core/stardist/tests/main.nf.test.snap @@ -0,0 +1,168 @@ +{ + "stardist2d - tif - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.stardist.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "STARDIST", + "stardist", + "0.9.2" + ] + ], + "2": [ + [ + "STARDIST", + "python", + "3.12.12" + ] + ], + "3": [ + [ + "STARDIST", + "tensorflow", + "2.20.0" + ] + ], + "4": [ + [ + "STARDIST", + "tifffile", + "2026.3.3" + ] + ], + "mask": [ + [ + { + "id": "test" + }, + "test.stardist.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_python": [ + [ + "STARDIST", + "python", + "3.12.12" + ] + ], + "versions_stardist": [ + [ + "STARDIST", + "stardist", + "0.9.2" + ] + ], + "versions_tensorflow": [ + [ + "STARDIST", + "tensorflow", + "2.20.0" + ] + ], + "versions_tifffile": [ + [ + "STARDIST", + "tifffile", + "2026.3.3" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-04T22:33:02.205105908" + }, + "stardist2d - tif": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "nuclear_image.stardist.tif:md5,ca29a05346d9e0d4c15bb133122560ce" + ] + ], + "1": [ + [ + "STARDIST", + "stardist", + "0.9.2" + ] + ], + "2": [ + [ + "STARDIST", + "python", + "3.12.12" + ] + ], + "3": [ + [ + "STARDIST", + "tensorflow", + "2.20.0" + ] + ], + "4": [ + [ + "STARDIST", + "tifffile", + "2026.3.3" + ] + ], + "mask": [ + [ + { + "id": "test" + }, + "nuclear_image.stardist.tif:md5,ca29a05346d9e0d4c15bb133122560ce" + ] + ], + "versions_python": [ + [ + "STARDIST", + "python", + "3.12.12" + ] + ], + "versions_stardist": [ + [ + "STARDIST", + "stardist", + "0.9.2" + ] + ], + "versions_tensorflow": [ + [ + "STARDIST", + "tensorflow", + "2.20.0" + ] + ], + "versions_tifffile": [ + [ + "STARDIST", + "tifffile", + "2026.3.3" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-06T15:21:31.45100204" + } +} \ No newline at end of file diff --git a/modules/nf-core/stardist/tests/nextflow.config b/modules/nf-core/stardist/tests/nextflow.config new file mode 100644 index 00000000..5926218d --- /dev/null +++ b/modules/nf-core/stardist/tests/nextflow.config @@ -0,0 +1,3 @@ +docker { + fixOwnership = true +} diff --git a/subworkflows/local/segmentation/main.nf b/subworkflows/local/segmentation/main.nf new file mode 100644 index 00000000..169bd75b --- /dev/null +++ b/subworkflows/local/segmentation/main.nf @@ -0,0 +1,52 @@ +// +// Cell segmentation of the tissue image +// + +include { IMAGE_DOWNSCALE } from "../../../modules/local/image/downscale" +include { CELLPOSE } from "../../../modules/nf-core/cellpose" +include { STARDIST } from "../../../modules/nf-core/stardist" +include { MASK_TO_GEOJSON } from "../../../modules/local/segmentation/mask_to_geojson" + +workflow SEGMENTATION { + + take: + ch_image // channel: [ meta, image ] + segmentation_method // string: cellpose or stardist + segmentation_downscale // integer: Downscale factor for the image + + main: + + IMAGE_DOWNSCALE ( + ch_image, + segmentation_downscale + ) + + ch_mask = channel.empty() + object_class = 'nucleus' + if (segmentation_method == 'cellpose') { + CELLPOSE ( + IMAGE_DOWNSCALE.out.image, + [] + ) + ch_mask = CELLPOSE.out.mask + object_class = 'cell' + } else if (segmentation_method == 'stardist') { + STARDIST ( + IMAGE_DOWNSCALE.out.image, + ['2D_versatile_he', []] + ) + ch_mask = STARDIST.out.mask + } else { + error("Unsupported segmentation_method '${segmentation_method}': expected 'cellpose' or 'stardist'") + } + + MASK_TO_GEOJSON ( + ch_mask, + segmentation_downscale, + object_class + ) + + emit: + mask = ch_mask // channel: [ meta, tif ] + geojson = MASK_TO_GEOJSON.out.geojson // channel: [ meta, geojson ] +} From b67640d58b67dbcdb715db827784d53b4b26c378 Mon Sep 17 00:00:00 2001 From: Christophe Avenel Date: Sun, 11 Oct 2026 23:40:41 +0200 Subject: [PATCH 4/7] Add cell segmentation for Visium HD New --segmentation_method (spaceranger, cellpose, stardist) and a samplesheet `segmentation_file` column. When either is given, cells replace bins as the analysis unit; the bin table is kept in the SpatialData object. - Raw data: cellpose/stardist segment the tissue image and the result is passed to Space Ranger with --custom-segmentation-file. Whole-cell segmentations (cellpose) are not expanded. - Processed data: Space Ranger's own segmentation is read, or bins are grouped into cells with bin2cell. - Space Ranger's nucleus segmentation is turned off for Visium HD unless cells are requested. - Segmentation runs at full image resolution by default; test profiles downscale, since their tissue image is full size. - Input validation for segmentation on non-HD or incomplete output, and a clear error when no cell table or no cells are produced. - Spatial neighbours use generic coordinates for cells. --- bin/report.qmd | 15 +++- conf/modules.config | 37 +++++++- conf/test.config | 1 + conf/test_downstream.config | 1 + conf/test_skip_downstream.config | 1 + conf/test_spaceranger_hd.config | 1 + conf/test_spaceranger_v1.config | 1 + main.nf | 6 ++ modules/local/adata/extend/tests/main.nf.test | 38 ++++---- modules/local/sdata/read_visium/main.nf | 2 +- .../read_visium/templates/read_visium.py | 48 ++++++++-- .../sdata/read_visium/tests/main.nf.test | 8 +- .../interaction_matrix/tests/main.nf.test | 33 ++++--- .../nhood_enrichment/tests/main.nf.test | 33 ++++--- .../spatial_autocorr/tests/main.nf.test | 55 ++++++------ .../local/squidpy/spatial_neighbors/main.nf | 3 +- .../spatial_neighbors/tests/main.nf.test | 44 +++++---- modules/nf-core/spaceranger/count/main.nf | 4 +- modules/nf-core/spaceranger/count/meta.yml | 7 ++ .../spaceranger/count/spaceranger-count.diff | 84 ++++++++++++++++- .../spaceranger/count/tests/main.nf.test | 8 +- nextflow.config | 5 ++ nextflow_schema.json | 35 ++++++++ subworkflows/local/input_check/main.nf | 89 +++++++++++++++++-- subworkflows/local/spatial/main.nf | 4 +- workflows/spatialvi.nf | 54 +++++++++-- 26 files changed, 471 insertions(+), 146 deletions(-) diff --git a/bin/report.qmd b/bin/report.qmd index 22eb0d45..3aec26e2 100644 --- a/bin/report.qmd +++ b/bin/report.qmd @@ -129,9 +129,18 @@ def display_table(table, hide_index=True, format_dict=None): # Load SpatialData sdata = spatialdata.read_zarr(input_sdata) -# Get the table (assuming single sample, take first table) -table_names = list(sdata.tables.keys()) -table_name = table_names[0] +# Get the main table (assuming single sample; skip the Visium HD bin table, +# which only exists next to a "_table" of cells) +table_name = next( + ( + t for t in sdata.tables + if t.endswith("_table") + and not (t.endswith("_bin_table") and t[: -len("_bin_table")] + "_table" in sdata.tables) + ), + None, +) +if table_name is None: + raise ValueError(f"No main table in SpatialData object; tables present: {list(sdata.tables)}") adata = sdata.tables[table_name] # Extract sample ID from table name diff --git a/conf/modules.config b/conf/modules.config index 86ef1313..918a46e4 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -39,7 +39,12 @@ process { } withName: SPACERANGER_COUNT { - ext.args = '--create-bam="false"' + // cellpose gives whole cells, which are not expanded; HD without cells skips segmentation + ext.args = { [ + '--create-bam="false"', + segmentation ? "--nucleus-expansion-distance-micron=${params.segmentation_method == 'cellpose' ? 0 : params.segmentation_expansion_distance}" : '', + (meta.hd && !meta.cells) ? '--nucleus-segmentation=false' : '' + ].join(' ') } publishDir = [ path: { "${params.outdir}/${meta.id}/spaceranger" }, mode: params.publish_dir_mode, @@ -57,6 +62,36 @@ process { time = { 4.h * task.attempt } } + withName: 'CELLPOSE' { + ext.args = '--no_npy' + // Cellpose-SAM needs a GPU for Visium HD; it will not finish on CPU + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 8.h * task.attempt } + // cellpose writes the mask into a per-sample subdirectory + publishDir = [ + path: { "${params.outdir}/${meta.id}/segmentation" }, + mode: params.publish_dir_mode, + pattern: "**/*masks.tif", + saveAs: { filename -> filename.tokenize('/').last() } + ] + } + + withName: 'STARDIST' { + // Full-resolution prediction peaks above process_medium + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 8.h * task.attempt } + } + + withName: 'STARDIST|MASK_TO_GEOJSON' { + publishDir = [ + path: { "${params.outdir}/${meta.id}/segmentation" }, + mode: params.publish_dir_mode, + pattern: "*.{tif,geojson}" + ] + } + withName: FASTQC { publishDir = [ path: { "${params.outdir}/${meta.id}/fastqc" }, diff --git a/conf/test.config b/conf/test.config index cdfc5249..1a03ddee 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,6 +23,7 @@ params { config_profile_description = 'Test pipeline functionality, including Space Ranger v2' // Input and output + segmentation_downscale = 4 // test images are full resolution; keep segmentation fast input = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_spaceranger.csv" spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs/probe_set.csv" spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/homo_sapiens_chr22_reference.tar.gz" diff --git a/conf/test_downstream.config b/conf/test_downstream.config index e31a2da7..b0f9ea77 100644 --- a/conf/test_downstream.config +++ b/conf/test_downstream.config @@ -23,6 +23,7 @@ params { config_profile_description = 'Test pipeline for downstream (post-Space Ranger) functionality' // Input and output + segmentation_downscale = 4 // test images are full resolution; keep segmentation fast input = 'https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_downstream.csv' spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs/probe_set.csv" spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/homo_sapiens_chr22_reference.tar.gz" diff --git a/conf/test_skip_downstream.config b/conf/test_skip_downstream.config index 567706b8..d8fdcbf8 100644 --- a/conf/test_skip_downstream.config +++ b/conf/test_skip_downstream.config @@ -23,6 +23,7 @@ params { config_profile_description = 'Test pipeline with skipping of all downstream steps' // Input and output + segmentation_downscale = 4 // test images are full resolution; keep segmentation fast input = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/samplesheet_spaceranger.csv" spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/outs/probe_set.csv" spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/homo_sapiens_chr22_reference.tar.gz" diff --git a/conf/test_spaceranger_hd.config b/conf/test_spaceranger_hd.config index 06d8c5fb..6d5d6683 100644 --- a/conf/test_spaceranger_hd.config +++ b/conf/test_spaceranger_hd.config @@ -23,6 +23,7 @@ params { config_profile_description = 'Test pipeline functionality on Visium HD file' // Input and output + segmentation_downscale = 4 // test images are full resolution; keep segmentation fast input = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-lung-cancer-post-xenium_hd_ffpe/samplesheet_spaceranger_hd.csv" spaceranger_probeset = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-lung-cancer-post-xenium_hd_ffpe/Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_probe_set.csv" spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/GRCh38.tar.gz" diff --git a/conf/test_spaceranger_v1.config b/conf/test_spaceranger_v1.config index 5411a1a4..bf93cc05 100644 --- a/conf/test_spaceranger_v1.config +++ b/conf/test_spaceranger_v1.config @@ -23,6 +23,7 @@ params { config_profile_description = 'Test pipeline functionality, including Space Ranger v1' // Input and output + segmentation_downscale = 4 // test images are full resolution; keep segmentation fast input = 'https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-ovarian-cancer-1-standard_v1_ffpe/samplesheet_spaceranger.csv' spaceranger_probeset = 'https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/human-ovarian-cancer-1-standard_v1_ffpe/Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv' spaceranger_reference = "https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/testdata/homo_sapiens_chr22_reference.tar.gz" diff --git a/main.nf b/main.nf index a067338b..ae1bfef9 100644 --- a/main.nf +++ b/main.nf @@ -34,6 +34,8 @@ workflow NFCORE_SPATIALVI { spaceranger_reference // dir: /path/to/reference spaceranger_probeset // file: /path/to/csv hd_bin_size // integer: Bin size for Visium HD + segmentation_method // string: Cell segmentation method (Visium HD) + segmentation_downscale // integer: Downscale factor of the image for segmentation skip_downstream // boolean: Whether to skip downstream steps or not qc_min_counts // integer: Minimum UMIs per spot qc_min_genes // integer: Minimum genes per spot @@ -73,6 +75,8 @@ workflow NFCORE_SPATIALVI { spaceranger_reference, spaceranger_probeset, hd_bin_size, + segmentation_method, + segmentation_downscale, skip_downstream, qc_min_counts, qc_min_genes, @@ -137,6 +141,8 @@ workflow { params.spaceranger_reference, params.spaceranger_probeset, params.hd_bin_size, + params.segmentation_method, + params.segmentation_downscale, params.skip_downstream, params.qc_min_counts, params.qc_min_genes, diff --git a/modules/local/adata/extend/tests/main.nf.test b/modules/local/adata/extend/tests/main.nf.test index db96626d..bb99de22 100644 --- a/modules/local/adata/extend/tests/main.nf.test +++ b/modules/local/adata/extend/tests/main.nf.test @@ -299,8 +299,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -316,10 +316,9 @@ nextflow_process { script "../../../squidpy/spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -379,8 +378,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -396,10 +395,9 @@ nextflow_process { script "../../../squidpy/spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -1117,8 +1115,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -1198,8 +1196,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -1273,8 +1271,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -1328,8 +1326,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } diff --git a/modules/local/sdata/read_visium/main.nf b/modules/local/sdata/read_visium/main.nf index a0a5e860..962db32f 100644 --- a/modules/local/sdata/read_visium/main.nf +++ b/modules/local/sdata/read_visium/main.nf @@ -5,7 +5,7 @@ process SDATA_READ_VISIUM { container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: - tuple val(meta), path(spaceranger_dir, arity: '1') + tuple val(meta), path(spaceranger_dir, arity: '1'), val(read_cells) val(hd_bin_size) output: diff --git a/modules/local/sdata/read_visium/templates/read_visium.py b/modules/local/sdata/read_visium/templates/read_visium.py index 9559d745..c7c24591 100644 --- a/modules/local/sdata/read_visium/templates/read_visium.py +++ b/modules/local/sdata/read_visium/templates/read_visium.py @@ -19,6 +19,7 @@ import re import shutil +import h5py import spatialdata_io import yaml from threadpoolctl import threadpool_limits @@ -30,8 +31,9 @@ threadpool_limits(int("${task.cpus}")) -def read_visium_hd(spaceranger_dir, sample_id_clean, hd_bin_size): - """Read Visium HD data.""" +def read_visium_hd(spaceranger_dir, sample_id_clean, hd_bin_size, use_cells): + """Read Visium HD data. Uses the Space Ranger cell segmentation as main + table when cells were requested and the segmentation is present.""" logger.info(f"Reading Visium HD data with bin size: {hd_bin_size}") # Add sample ID to feature_slice, if not present @@ -46,13 +48,45 @@ def read_visium_hd(spaceranger_dir, sample_id_clean, hd_bin_size): logger.info(f"Copying {feature_slice_src} to {feature_slice_dst}") shutil.copyfile(feature_slice_src, feature_slice_dst) + # An empty cell matrix fails obscurely inside spatialdata_io, so say it here + cell_matrix = os.path.join( + spaceranger_dir, "segmented_outputs", "filtered_feature_cell_matrix.h5" + ) + if use_cells and os.path.exists(cell_matrix): + with h5py.File(cell_matrix, "r") as f: + if f["matrix/barcodes"].shape is None or f["matrix/barcodes"].shape[0] == 0: + raise ValueError( + f"Space Ranger produced no cells from the segmentation in " + f"{spaceranger_dir}. Check that the segmentation covers the " + f"tissue and is in full-resolution image pixels." + ) + sdata = spatialdata_io.visium_hd( spaceranger_dir, bin_size=[hd_bin_size], dataset_id=sample_id_clean, + load_segmentations_only=False, ) table_name = f"square_{hd_bin_size:03d}um" + cell_table = "cell_segmentations" + + if use_cells: + if cell_table not in sdata.tables: + raise ValueError( + f"Cells were requested but no cell table was found in " + f"{spaceranger_dir}/segmented_outputs. " + f"Tables present: {sorted(sdata.tables)}" + ) + logger.info(f"Using cell segmentation table {cell_table!r} as main table") + sdata.tables[f"{sample_id_clean}_bin_table"] = sdata.tables[table_name] + del sdata.tables[table_name] + table_name = cell_table + elif cell_table in sdata.tables: + # Bins are the analysis unit, so drop the unused cell table + logger.info(f"Removing unused table {cell_table!r}") + del sdata.tables[cell_table] + return sdata, table_name @@ -68,7 +102,7 @@ def read_visium_standard(spaceranger_dir, sample_id_clean): return sdata, table_name -def read_visium_data(spaceranger_dir, sample_id_clean, hd_bin_size): +def read_visium_data(spaceranger_dir, sample_id_clean, hd_bin_size, use_cells): """Read Visium or Visium HD data from Space Ranger output.""" logger.info(f"Reading data from: {spaceranger_dir}") logger.info(f"Sample ID: {sample_id_clean}") @@ -80,7 +114,8 @@ def read_visium_data(spaceranger_dir, sample_id_clean, hd_bin_size): sdata, table_name = read_visium_hd( spaceranger_dir, sample_id_clean, - hd_bin_size + hd_bin_size, + use_cells ) else: sdata, table_name = read_visium_standard( @@ -151,6 +186,8 @@ def main(): spaceranger_dir = "${spaceranger_dir}" sample_id = "${meta.id}" hd_bin_size = int("${hd_bin_size}") + # Read Space Ranger's cell table instead of bins + use_cells = "${read_cells}" == "true" output_sdata = "${prefix}.zarr" process_name = "${task.process}" @@ -160,7 +197,8 @@ def main(): sdata, table_name = read_visium_data( spaceranger_dir, sample_id_clean, - hd_bin_size + hd_bin_size, + use_cells ) sdata = validate_table(sdata, table_name, sample_id_clean) diff --git a/modules/local/sdata/read_visium/tests/main.nf.test b/modules/local/sdata/read_visium/tests/main.nf.test index 1ace6a81..67031178 100644 --- a/modules/local/sdata/read_visium/tests/main.nf.test +++ b/modules/local/sdata/read_visium/tests/main.nf.test @@ -27,8 +27,8 @@ nextflow_process { when { process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -77,8 +77,8 @@ nextflow_process { when { process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } diff --git a/modules/local/squidpy/interaction_matrix/tests/main.nf.test b/modules/local/squidpy/interaction_matrix/tests/main.nf.test index f2f7472f..bb4202af 100644 --- a/modules/local/squidpy/interaction_matrix/tests/main.nf.test +++ b/modules/local/squidpy/interaction_matrix/tests/main.nf.test @@ -25,8 +25,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -42,10 +42,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = "grid" // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, "grid"] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -125,8 +124,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -142,10 +141,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = "grid" // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, "grid"] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -227,8 +225,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -244,10 +242,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = "grid" // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, "grid"] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } diff --git a/modules/local/squidpy/nhood_enrichment/tests/main.nf.test b/modules/local/squidpy/nhood_enrichment/tests/main.nf.test index 54838621..f0c698fe 100644 --- a/modules/local/squidpy/nhood_enrichment/tests/main.nf.test +++ b/modules/local/squidpy/nhood_enrichment/tests/main.nf.test @@ -25,8 +25,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -42,10 +42,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = "grid" // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, "grid"] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -125,8 +124,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -142,10 +141,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = "grid" // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, "grid"] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -227,8 +225,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -244,10 +242,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = "grid" // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, "grid"] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } diff --git a/modules/local/squidpy/spatial_autocorr/tests/main.nf.test b/modules/local/squidpy/spatial_autocorr/tests/main.nf.test index 0d1f2616..524cbf6f 100644 --- a/modules/local/squidpy/spatial_autocorr/tests/main.nf.test +++ b/modules/local/squidpy/spatial_autocorr/tests/main.nf.test @@ -25,8 +25,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -42,10 +42,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -91,8 +90,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -108,10 +107,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -157,8 +155,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -174,10 +172,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -223,8 +220,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -240,10 +237,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -294,8 +290,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -311,10 +307,9 @@ nextflow_process { script "../../spatial_neighbors/main.nf" process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } diff --git a/modules/local/squidpy/spatial_neighbors/main.nf b/modules/local/squidpy/spatial_neighbors/main.nf index 94e9df88..96274603 100644 --- a/modules/local/squidpy/spatial_neighbors/main.nf +++ b/modules/local/squidpy/spatial_neighbors/main.nf @@ -5,8 +5,7 @@ process SQUIDPY_SPATIAL_NEIGHBORS { container "community.wave.seqera.io/library/bin2cell_harmonypy_scanorama_imagecodecs_pruned:d457f4c6ebb7b325" input: - tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1') - val coord_type + tuple val(meta), path(adata, stageAs: "input.h5ad", arity: '1'), val(coord_type) val n_neighs val write_adata diff --git a/modules/local/squidpy/spatial_neighbors/tests/main.nf.test b/modules/local/squidpy/spatial_neighbors/tests/main.nf.test index 93cb8815..6d2b306a 100644 --- a/modules/local/squidpy/spatial_neighbors/tests/main.nf.test +++ b/modules/local/squidpy/spatial_neighbors/tests/main.nf.test @@ -25,8 +25,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -43,10 +43,9 @@ nextflow_process { when { process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -81,8 +80,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -99,10 +98,9 @@ nextflow_process { when { process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = false // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = false // write_adata """ } } @@ -137,8 +135,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -155,10 +153,9 @@ nextflow_process { when { process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'generic' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'generic'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } @@ -195,8 +192,8 @@ nextflow_process { script "../../../sdata/read_visium/main.nf" process { """ - input[0] = UNTAR.out.untar - input[1] = 8 // hd_bin_size + input[0] = UNTAR.out.untar.map { meta, dir -> [meta, dir, false] } + input[1] = 8 // hd_bin_size """ } } @@ -213,10 +210,9 @@ nextflow_process { when { process { """ - input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata - input[1] = 'grid' // coord_type - input[2] = 6 // n_neighs - input[3] = true // write_adata + input[0] = SDATA_TO_LEGACY_ANNDATA.out.adata.map { meta, adata -> [meta, adata, 'grid'] } + input[1] = 6 // n_neighs + input[2] = true // write_adata """ } } diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf index f8589b93..58674048 100644 --- a/modules/nf-core/spaceranger/count/main.nf +++ b/modules/nf-core/spaceranger/count/main.nf @@ -5,7 +5,7 @@ process SPACERANGER_COUNT { container "quay.io/nf-core/spaceranger:9c5e7dc93c32448e" input: - tuple val(meta), path(reads), path(image), val(slide), val(area), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile) + tuple val(meta), path(reads), path(image), val(slide), val(area), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile), path(segmentation) path(reference) path(probeset) @@ -27,6 +27,7 @@ process SPACERANGER_COUNT { def probeset_opt = probeset ? "--probe-set=\"${probeset}\"" : "" def alignment_opt = alignment ? "--loupe-alignment=\"${alignment}\"" : "" def slidefile_opt = slidefile ? "--slidefile=\"${slidefile}\"" : "" + def segmentation_opt = segmentation ? "--custom-segmentation-file=\"${segmentation}\"" : "" def image_opt = image ? "--image=\"${image}\"" : "" def cytaimage_opt = cytaimage ? "--cytaimage=\"${cytaimage}\"" : "" def darkimage_opt = darkimage ? "--darkimage=\"${darkimage}\"" : "" @@ -52,6 +53,7 @@ process SPACERANGER_COUNT { $probeset_opt \\ $alignment_opt \\ $slidefile_opt \\ + $segmentation_opt \\ $args mv ${prefix}/outs outs """ diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml index 054f0047..9cf17658 100644 --- a/modules/nf-core/spaceranger/count/meta.yml +++ b/modules/nf-core/spaceranger/count/meta.yml @@ -83,6 +83,13 @@ input: pattern: "*.json" ontologies: - edam: http://edamontology.org/format_3464 # JSON + - segmentation: + type: file + description: OPTIONAL - Custom cell or nucleus segmentation (GeoJSON or + label mask) in full-resolution image pixels, passed as + --custom-segmentation-file + pattern: "*.{geojson,tif,tiff,npy}" + ontologies: [] - reference: type: directory description: Folder containing all the reference indices needed by Space diff --git a/modules/nf-core/spaceranger/count/spaceranger-count.diff b/modules/nf-core/spaceranger/count/spaceranger-count.diff index 0b43fc99..71015cb8 100644 --- a/modules/nf-core/spaceranger/count/spaceranger-count.diff +++ b/modules/nf-core/spaceranger/count/spaceranger-count.diff @@ -1,9 +1,14 @@ Changes in component 'nf-core/spaceranger/count' -'modules/nf-core/spaceranger/count/meta.yml' is unchanged Changes in 'spaceranger/count/main.nf': --- modules/nf-core/spaceranger/count/main.nf +++ modules/nf-core/spaceranger/count/main.nf -@@ -10,7 +10,7 @@ +@@ -5,12 +5,12 @@ + container "quay.io/nf-core/spaceranger:9c5e7dc93c32448e" + + input: +- tuple val(meta), path(reads), path(image), val(slide), val(area), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile) ++ tuple val(meta), path(reads), path(image), val(slide), val(area), path(cytaimage), path(darkimage), path(colorizedimage), path(alignment), path(slidefile), path(segmentation) + path(reference) path(probeset) output: @@ -12,8 +17,81 @@ Changes in 'spaceranger/count/main.nf': tuple val("${task.process}"), val('spaceranger'), eval('spaceranger -V | sed "s/spaceranger spaceranger-//"'), emit: versions_spaceranger, topic: versions when: +@@ -27,6 +27,7 @@ + def probeset_opt = probeset ? "--probe-set=\"${probeset}\"" : "" + def alignment_opt = alignment ? "--loupe-alignment=\"${alignment}\"" : "" + def slidefile_opt = slidefile ? "--slidefile=\"${slidefile}\"" : "" ++ def segmentation_opt = segmentation ? "--custom-segmentation-file=\"${segmentation}\"" : "" + def image_opt = image ? "--image=\"${image}\"" : "" + def cytaimage_opt = cytaimage ? "--cytaimage=\"${cytaimage}\"" : "" + def darkimage_opt = darkimage ? "--darkimage=\"${darkimage}\"" : "" +@@ -52,6 +53,7 @@ + $probeset_opt \\ + $alignment_opt \\ + $slidefile_opt \\ ++ $segmentation_opt \\ + $args + mv ${prefix}/outs outs + """ + +Changes in 'spaceranger/count/meta.yml': +--- modules/nf-core/spaceranger/count/meta.yml ++++ modules/nf-core/spaceranger/count/meta.yml +@@ -83,6 +83,13 @@ + pattern: "*.json" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON ++ - segmentation: ++ type: file ++ description: OPTIONAL - Custom cell or nucleus segmentation (GeoJSON or ++ label mask) in full-resolution image pixels, passed as ++ --custom-segmentation-file ++ pattern: "*.{geojson,tif,tiff,npy}" ++ ontologies: [] + - reference: + type: directory + description: Folder containing all the reference indices needed by Space + +Changes in 'spaceranger/count/tests/main.nf.test': +--- modules/nf-core/spaceranger/count/tests/main.nf.test ++++ modules/nf-core/spaceranger/count/tests/main.nf.test +@@ -57,6 +57,7 @@ + [], // Colorizedimage + [], // Manual alignment (default: automatic alignment) + [], // Slide specification (default: automatic download) ++ [], // Custom segmentation (default: none) + ] + input[1] = SPACERANGER_MKREF.out.reference // Reference + input[2] = [] // Probeset (default: use the one included with Space Ranger) +@@ -137,6 +138,7 @@ + [], // Colorizedimage + [], // Manual alignment (default: automatic alignment) + [], // Slide specification (default: automatic download) ++ [], // Custom segmentation (default: none) + ] + input[1] = SPACERANGER_MKREF.out.reference // Reference + input[2] = [] // Probeset (default: use the one included with Space Ranger) +@@ -195,7 +197,8 @@ + [], // Darkimage + [], // Colorizedimage + [], // Manual alignment (default: automatic alignment) +- file('https://s3.us-west-2.amazonaws.com/10x.spatial-slides/gpr/V52Y10/V52Y10-317.gpr') // Slide specification (default: automatic download) ++ file('https://s3.us-west-2.amazonaws.com/10x.spatial-slides/gpr/V52Y10/V52Y10-317.gpr'), // Slide specification (default: automatic download) ++ [] // Custom segmentation (default: none) + ] + input[1] = SPACERANGER_MKREF.out.reference // Reference + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv', checkIfExists: true) // Probeset (default: use the one included with Space Ranger) +@@ -274,7 +277,8 @@ + [], // Darkimage + [], // Colorizedimage + [], // Manual alignment (default: automatic alignment) +- [] // Slide specification (default: automatic download) ++ [], // Slide specification (default: automatic download) ++ [] // Custom segmentation (default: none) + ] + input[1] = SPACERANGER_MKREF.out.reference // Reference + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-lung-cancer-post-xenium_hd_ffpe/Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_probe_set.csv', checkIfExists: true) // Probeset (default: use the one included with Space Ranger) 'modules/nf-core/spaceranger/count/tests/main.nf.test.snap' is unchanged 'modules/nf-core/spaceranger/count/tests/nextflow.config' is unchanged -'modules/nf-core/spaceranger/count/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test b/modules/nf-core/spaceranger/count/tests/main.nf.test index e8addc87..db53b1c5 100644 --- a/modules/nf-core/spaceranger/count/tests/main.nf.test +++ b/modules/nf-core/spaceranger/count/tests/main.nf.test @@ -57,6 +57,7 @@ nextflow_process { [], // Colorizedimage [], // Manual alignment (default: automatic alignment) [], // Slide specification (default: automatic download) + [], // Custom segmentation (default: none) ] input[1] = SPACERANGER_MKREF.out.reference // Reference input[2] = [] // Probeset (default: use the one included with Space Ranger) @@ -137,6 +138,7 @@ nextflow_process { [], // Colorizedimage [], // Manual alignment (default: automatic alignment) [], // Slide specification (default: automatic download) + [], // Custom segmentation (default: none) ] input[1] = SPACERANGER_MKREF.out.reference // Reference input[2] = [] // Probeset (default: use the one included with Space Ranger) @@ -195,7 +197,8 @@ nextflow_process { [], // Darkimage [], // Colorizedimage [], // Manual alignment (default: automatic alignment) - file('https://s3.us-west-2.amazonaws.com/10x.spatial-slides/gpr/V52Y10/V52Y10-317.gpr') // Slide specification (default: automatic download) + file('https://s3.us-west-2.amazonaws.com/10x.spatial-slides/gpr/V52Y10/V52Y10-317.gpr'), // Slide specification (default: automatic download) + [] // Custom segmentation (default: none) ] input[1] = SPACERANGER_MKREF.out.reference // Reference input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv', checkIfExists: true) // Probeset (default: use the one included with Space Ranger) @@ -274,7 +277,8 @@ nextflow_process { [], // Darkimage [], // Colorizedimage [], // Manual alignment (default: automatic alignment) - [] // Slide specification (default: automatic download) + [], // Slide specification (default: automatic download) + [] // Custom segmentation (default: none) ] input[1] = SPACERANGER_MKREF.out.reference // Reference input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-lung-cancer-post-xenium_hd_ffpe/Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_probe_set.csv', checkIfExists: true) // Probeset (default: use the one included with Space Ranger) diff --git a/nextflow.config b/nextflow.config index bc335e46..2cc5e090 100644 --- a/nextflow.config +++ b/nextflow.config @@ -19,6 +19,11 @@ params { // Visium HD options hd_bin_size = 8 + // Segmentation options + segmentation_method = null + segmentation_downscale = 1 + segmentation_expansion_distance = 5 + // Filtering options qc_min_counts = 500 qc_min_genes = 250 diff --git a/nextflow_schema.json b/nextflow_schema.json index e94d9eaf..67e9e2a1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -87,6 +87,38 @@ } }, + "segmentation_options": { + "title": "Segmentation options", + "type": "object", + "fa_icon": "fas fa-draw-polygon", + "description": "Options for cell segmentation of Visium HD data.", + "properties": { + "segmentation_method": { + "type": "string", + "enum": ["spaceranger", "cellpose", "stardist"], + "description": "Cell segmentation method for Visium HD: Space Ranger's own nucleus segmentation (`spaceranger`), or `cellpose` or `stardist` on the tissue image. Cannot be combined with a `segmentation_file` in the samplesheet.", + "help_text": "When set, cells replace bins as the analysis unit. `cellpose` and `stardist` segment the samplesheet `image`; for raw data the result is passed to Space Ranger, for processed data the 2 µm bins are grouped into cells with bin2cell. `cellpose` needs a GPU (`-profile gpu`) on full-size Visium HD images.", + "fa_icon": "fas fa-draw-polygon" + }, + "segmentation_downscale": { + "type": "integer", + "default": 1, + "minimum": 1, + "description": "Downscale factor of the tissue image before running cellpose or stardist. The default of 1 segments at full resolution; larger values are faster but detect far fewer nuclei.", + "help_text": "The segmentation is scaled back to full-resolution pixels afterwards. Use values above 1 only for quick tests.", + "fa_icon": "fas fa-compress" + }, + "segmentation_expansion_distance": { + "type": "number", + "default": 5, + "minimum": 0, + "description": "Distance in microns by which Space Ranger expands nuclei into cells, for `stardist` or a nucleus `segmentation_file`. Not applied to `cellpose`, which segments whole cells. On the bin2cell path nuclei are expanded with bin2cell defaults.", + "help_text": "Only used when Space Ranger runs on raw data. Set to 0 to use the nuclei as they are.", + "fa_icon": "fas fa-arrows-alt" + } + } + }, + "filtering_options": { "title": "Filtering options", "type": "object", @@ -517,6 +549,9 @@ { "$ref": "#/$defs/visium_hd_options" }, + { + "$ref": "#/$defs/segmentation_options" + }, { "$ref": "#/$defs/filtering_options" }, diff --git a/subworkflows/local/input_check/main.nf b/subworkflows/local/input_check/main.nf index d57609d6..3ecb7172 100644 --- a/subworkflows/local/input_check/main.nf +++ b/subworkflows/local/input_check/main.nf @@ -8,13 +8,15 @@ include { UNTAR as UNTAR_DOWNSTREAM_INPUT } from "../../../modules/nf-core/unta workflow INPUT_CHECK { take: - samplesheet // file: samplesheet read in from --input - hd_bin_size // integer: Bin size for Visium HD + samplesheet // file: samplesheet read in from --input + hd_bin_size // integer: Bin size for Visium HD + segmentation_method // string: Segmentation method, if any main: ch_st = channel.fromPath(samplesheet) .splitCsv ( header: true, sep: ',') + .map { it -> check_segmentation(it, segmentation_method) } .branch { it -> spaceranger: !it.containsKey("spaceranger_dir") downstream: it.containsKey("spaceranger_dir") @@ -38,7 +40,7 @@ workflow INPUT_CHECK { .mix ( ch_spaceranger.dir.map { meta, dir -> [meta, file(dir)] } ) // Create final meta map and check input existance ch_spaceranger_input = ch_spaceranger_combined - .map { meta, dir -> create_channel_spaceranger(meta, dir) } + .map { meta, dir -> create_channel_spaceranger(meta, dir, segmentation_method) } // Downstream analysis: ---------------------------------------------------- @@ -60,11 +62,34 @@ workflow INPUT_CHECK { // Create final meta map and check input file existence ch_downstream_input = ch_downstream_combined - .map { it -> check_downstream_dir(it, hd_bin_size) } + .map { it -> check_downstream_dir(it, hd_bin_size, segmentation_method) } + + // Tissue images from both input modes + ch_image = ch_spaceranger_input + .map { it -> [it[0], it[2]] } + .mix ( ch_downstream_input.map { meta, _dir -> [meta, get_file_from_meta(meta, "image")] } ) + .filter { _meta, image -> image as boolean } + + // Segmentations supplied in the samplesheet, in full-resolution pixels + ch_segmentation_file = ch_spaceranger_input + .map { it -> it[0] } + .mix ( ch_downstream_input.map { meta, _dir -> meta } ) + .map { meta -> [meta, get_file_from_meta(meta, "segmentation_file")] } + .filter { _meta, segmentation -> segmentation as boolean } emit: ch_spaceranger_input // channel: [ val(meta), [ st data ] ] ch_downstream_input // channel: [ val(meta), [ st data ] ] + ch_image // channel: [ val(meta), image ] + ch_segmentation_file // channel: [ val(meta), segmentation ] +} + +// Function: `segmentation_file` and `--segmentation_method` are mutually exclusive +def check_segmentation(meta, segmentation_method) { + if (segmentation_method && meta.get('segmentation_file')) { + error "Sample '${meta.sample}' has a `segmentation_file`, which cannot be combined with `--segmentation_method`." + } + return meta } // Function: normalize meta only (no filesystem checks) @@ -75,9 +100,18 @@ def create_channel_downstream(meta) { } // Function: validate that required files exist in the dir -def check_downstream_dir(input, hd_bin_size) { +def check_downstream_dir(input, hd_bin_size, segmentation_method) { def (meta, spaceranger_dir) = input + // Check for existence of optional files + def image = get_file_from_meta(meta, "image") + def segmentation_file = get_file_from_meta(meta, "segmentation_file") + ['image': image, 'segmentation_file': segmentation_file].each { k, f -> + if (f && !f.exists()) { + error "File for `${k}` is specified, but does not exist: ${f}." + } + } + // Non-HD SpaceRanger output required files def classic_required_files = [ "filtered_feature_bc_matrix.h5", @@ -106,9 +140,36 @@ def check_downstream_dir(input, hd_bin_size) { error "The specified spaceranger output directory for sample '${meta.id}' does not contain all required files for either classic Visium: ${classic_required_files.join(', ')} or Visium HD bin size ${hd_bin_size}: ${hd_required_files.join(', ')}." } + // Route flags: bin2cell groups the bins of processed data into cells + meta.hd = hd_files_present + meta.cells = (segmentation_file || segmentation_method) as boolean + meta.bin_to_cell = (segmentation_file || segmentation_method in ['cellpose', 'stardist']) as boolean + + // Cell segmentation is Visium HD only + if (meta.cells && !hd_files_present) { + error "Sample '${meta.id}': cell segmentation was requested but '${spaceranger_dir}' is classic Visium output. Segmentation is only supported for Visium HD." + } + check_segmentation_image(meta, image, segmentation_method) + if (meta.bin_to_cell) { + def bins_2um = "binned_outputs/square_002um/filtered_feature_bc_matrix.h5" + if (!file("${spaceranger_dir}/${bins_2um}").exists()) { + error "Sample '${meta.id}': grouping bins into cells needs the 2 µm bins, but '${spaceranger_dir}/${bins_2um}' is missing." + } + } + if (segmentation_method == 'spaceranger' && !file("${spaceranger_dir}/segmented_outputs").isDirectory()) { + error "Sample '${meta.id}': --segmentation_method spaceranger needs '${spaceranger_dir}/segmented_outputs', which is missing. Space Ranger 4.0 or later produces it for Visium HD." + } + return [meta, spaceranger_dir] } +// Function: cellpose and stardist segment the samplesheet `image` +def check_segmentation_image(meta, image, segmentation_method) { + if (segmentation_method in ['cellpose', 'stardist'] && !image) { + error "Sample '${meta.id}': `--segmentation_method ${segmentation_method}` needs an `image` in the samplesheet." + } +} + // Function to convert a path in `meta` to a file object and return it. If key // `k` is not contained in `meta` return an empty list which is recognized as // 'no file' by Nextflow. @@ -118,7 +179,7 @@ def get_file_from_meta(meta, k) { } // Function to get [ meta, [fastq_dir, tissue_hires_image, slide, area] ] list -def create_channel_spaceranger(meta, fastq_dir) { +def create_channel_spaceranger(meta, fastq_dir, segmentation_method) { meta["id"] = meta.get("sample") def slide = meta.get("slide") def area = meta.get("area") @@ -139,6 +200,7 @@ def create_channel_spaceranger(meta, fastq_dir) { def cytaimage = get_file_from_meta(meta, "cytaimage") def colorizedimage = get_file_from_meta(meta, "colorizedimage") def darkimage = get_file_from_meta(meta, "darkimage") + def segmentation_file = get_file_from_meta(meta, "segmentation_file") if(!fastq_files.size()) { error "No `fastq_dir` specified or no samples found in folder." @@ -151,7 +213,8 @@ def create_channel_spaceranger(meta, fastq_dir) { 'image': image, 'cytaimage': cytaimage, 'colorizedimage': colorizedimage, - 'darkimage': darkimage + 'darkimage': darkimage, + 'segmentation_file': segmentation_file ] optional_files.each { k, f -> if(f && !f.exists()) { @@ -164,5 +227,17 @@ def create_channel_spaceranger(meta, fastq_dir) { error "Need to specify at least one of 'image', 'cytaimage', 'colorizedimage', or 'darkimage' in the samplesheet" } + // Route flags: Space Ranger segments raw data itself, so never bin2cell + meta.hd = (slide?.startsWith('H1-') || (slidefile && slidefile.name.startsWith('H1-'))) as boolean + meta.cells = (segmentation_file || segmentation_method) as boolean + meta.bin_to_cell = false + + // Cell segmentation is Visium HD only; allowed when HD is undetectable + if (meta.cells && slide && !slide.startsWith('H1-')) { + error "Sample '${meta.id}': cell segmentation was requested but slide '${slide}' is classic Visium. Segmentation is only supported for Visium HD." + } + check_segmentation_image(meta, image, segmentation_method) + + // `segmentation_file` is emitted on its own channel, not in this tuple return [meta, fastq_files, image, slide, area, cytaimage, darkimage, colorizedimage, manual_alignment, slidefile] } diff --git a/subworkflows/local/spatial/main.nf b/subworkflows/local/spatial/main.nf index be914213..0a35e3ac 100644 --- a/subworkflows/local/spatial/main.nf +++ b/subworkflows/local/spatial/main.nf @@ -16,9 +16,9 @@ workflow SPATIAL { // // Spatial neighbors // + // Cells are irregular, so they always use generic coordinates SQUIDPY_SPATIAL_NEIGHBORS ( - ch_adata, - spatial_coord_type, + ch_adata.map { meta, h5ad -> [meta, h5ad, meta.cells ? 'generic' : spatial_coord_type] }, spatial_n_neighbors, true // write_adata ) diff --git a/workflows/spatialvi.nf b/workflows/spatialvi.nf index e7e36ad6..60c41235 100644 --- a/workflows/spatialvi.nf +++ b/workflows/spatialvi.nf @@ -5,6 +5,7 @@ */ include { SDATA_READ_VISIUM } from "../modules/local/sdata/read_visium" +include { SDATA_BIN_TO_CELL } from "../modules/local/sdata/bin_to_cell" include { FASTQC } from "../modules/nf-core/fastqc" include { ADATA_EXTEND } from "../modules/local/adata/extend" include { SCANPY_CALCULATE_QC_METRICS } from "../modules/local/scanpy/calculate_qc_metrics" @@ -17,6 +18,7 @@ include { QUARTO_NOTEBOOK as REPORT } from "../modules/nf-core/quarto/notebook include { SDATA_UPDATE_TABLE } from "../modules/local/sdata/update_table" include { INPUT_CHECK } from "../subworkflows/local/input_check" +include { SEGMENTATION } from "../subworkflows/local/segmentation" include { SPACERANGER } from "../subworkflows/local/spaceranger" include { PREPROCESSING } from "../subworkflows/local/preprocessing" include { CLUSTERING } from "../subworkflows/local/clustering" @@ -40,6 +42,8 @@ workflow SPATIALVI { spaceranger_reference // dir: /path/to/reference spaceranger_probeset // file: /path/to/csv hd_bin_size // integer: Bin size for Visium HD + segmentation_method // string: Cell segmentation method (Visium HD) + segmentation_downscale // integer: Downscale factor of the image for segmentation skip_downstream // boolean: Whether to skip downstream steps or not qc_min_counts // integer: Minimum UMIs per spot qc_min_genes // integer: Minimum genes per spot @@ -84,12 +88,36 @@ workflow SPATIALVI { // INPUT_CHECK ( samplesheet, - hd_bin_size + hd_bin_size, + segmentation_method ) + ch_spaceranger_input = INPUT_CHECK.out.ch_spaceranger_input + ch_downstream_input = INPUT_CHECK.out.ch_downstream_input + + // + // SUBWORKFLOW: Cell segmentation of the tissue image (Visium HD) + // + // Samplesheet and computed segmentations are both files in full-resolution pixels + ch_segmentation = INPUT_CHECK.out.ch_segmentation_file + if (segmentation_method in ['cellpose', 'stardist']) { + SEGMENTATION ( + INPUT_CHECK.out.ch_image, + segmentation_method, + segmentation_downscale + ) + ch_segmentation = ch_segmentation.mix ( SEGMENTATION.out.geojson ) + } + + // Attach the segmentation, or an empty list for samples without one + ch_spaceranger_input = ch_spaceranger_input + .join ( ch_segmentation, remainder: true ) // Space Ranger waits for the segmentation it is given + .filter { it -> it[1] != null } // drop segmentation-only rows + .map { it -> it[0..-2] + [it[-1] ?: []] } // // MODULE: FastQC // + // Read from INPUT_CHECK so FastQC does not wait for segmentation FASTQC( INPUT_CHECK.out.ch_spaceranger_input .map { it -> [it[0], it[1]] } // [ meta, reads ] @@ -101,7 +129,7 @@ workflow SPATIALVI { // SUBWORKFLOW: Space Ranger raw data processing // SPACERANGER ( - INPUT_CHECK.out.ch_spaceranger_input, + ch_spaceranger_input, spaceranger_reference, spaceranger_probeset, ) @@ -111,13 +139,29 @@ workflow SPATIALVI { // // MODULE: Read ST data and save as SpatialData // - ch_spaceranger_dir = INPUT_CHECK.out.ch_downstream_input + ch_spaceranger_dir = ch_downstream_input .mix(SPACERANGER.out.sr_dir) SDATA_READ_VISIUM ( - ch_spaceranger_dir, + ch_spaceranger_dir.map { meta, dir -> [meta, dir, meta.cells && !meta.bin_to_cell] }, + hd_bin_size + ) + + // + // MODULE: Group Visium HD bins into cells for processed data with a + // segmentation from cellpose, stardist or the samplesheet + // + ch_sdata = SDATA_READ_VISIUM.out.sdata + .branch { meta, _zarr -> + bin_to_cell: meta.bin_to_cell + other: true + } + SDATA_BIN_TO_CELL ( + ch_sdata.bin_to_cell + .join ( ch_downstream_input.filter { meta, _dir -> meta.bin_to_cell }, failOnMismatch: true ) + .join ( ch_segmentation.filter { meta, _seg -> meta.bin_to_cell }, failOnMismatch: true ), hd_bin_size ) - ch_sdata_raw = SDATA_READ_VISIUM.out.sdata + ch_sdata_raw = ch_sdata.other.mix(SDATA_BIN_TO_CELL.out.sdata) // ========================================================================= // PER-SAMPLE ANALYSES From 9116971a0937552b0d5bb543ef8e52f6c96abdf0 Mon Sep 17 00:00:00 2001 From: Christophe Avenel Date: Sun, 11 Oct 2026 23:40:41 +0200 Subject: [PATCH 5/7] Document cell segmentation for Visium HD --- CHANGELOG.md | 4 +++ CITATIONS.md | 16 ++++++++++++ README.md | 6 +++++ docs/output.md | 24 ++++++++++++++++++ docs/usage.md | 66 ++++++++++++++++++++++++++++++++++++++------------ 5 files changed, 100 insertions(+), 16 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 53d59d58..4703c376 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,10 @@ compatible with further downstream analyses and/or exploration in _e.g._ ### `Added` - Add pickled slot data outputs and `adata/extend`; don't output "raw" layer in raw data [[#153](https://github.com/nf-core/spatialvi/pull/153/)] +- Add optional Visium HD cell segmentation with Space Ranger, Cellpose, StarDist or a samplesheet `segmentation_file`, using cells instead of bins for the analysis [[#145](https://github.com/nf-core/spatialvi/issues/145) and [#161](https://github.com/nf-core/spatialvi/pull/161)] +- Turn off Space Ranger's nucleus segmentation for Visium HD unless cells are requested, so `segmented_outputs/` is no longer produced by default [[#161](https://github.com/nf-core/spatialvi/pull/161)] +- Move local modules to the SpatialData 0.8 stack (spatialdata-io 0.7, anndata 0.13) and add bin2cell [[#161](https://github.com/nf-core/spatialvi/pull/161)] +- Increase memory for per-sample steps on Visium HD data, and cap their time limit at 4 h per attempt [[#161](https://github.com/nf-core/spatialvi/pull/161)] - Deprecate `quartonotebook` module in favour of `quarto/notebook` [[#148](https://github.com/nf-core/spatialvi/pull/148)] - Separate reports into separate scripts [[#137](https://github.com/nf-core/spatialvi/pull/137)] - Use topic channels for software versions [[#133](https://github.com/nf-core/spatialvi/pull/133)] diff --git a/CITATIONS.md b/CITATIONS.md index fe4b5314..1689824b 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -14,6 +14,16 @@ > Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. bioRxiv 2021.12.16.473007; doi: https://doi.org/10.1101/2021.12.16.473007 +- [bin2cell](https://github.com/Teichlab/bin2cell) + + > Polański K, Bartolomé-Casado R, Sarropoulos I, Xu C, England N, Jahnsen FL, Teichmann SA, Yayon N. Bin2cell reconstructs cells from high resolution Visium HD data. Bioinformatics. 2024;40(9):btae546. doi: 10.1093/bioinformatics/btae546 + +- [Cellpose](https://github.com/MouseLand/cellpose) + + > Stringer C, Wang T, Michaelos M, Pachitariu M. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021). doi: 10.1038/s41592-020-01018-x + + > Pachitariu M, Rariden M, Stringer C. Cellpose-SAM: superhuman generalization for cellular segmentation. bioRxiv 2025.04.28.651001; doi: https://doi.org/10.1101/2025.04.28.651001 + - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. @@ -42,6 +52,12 @@ > Palla G, Spitzer H, Klein M et al. Squidpy: a scalable framework for spatial omics analysis. Nat Methods 19, 171–178 (2022). doi: https://doi.org/10.1038/s41592-021-01358-2 +- [StarDist](https://github.com/stardist/stardist) + + > Schmidt U, Weigert M, Broaddus C, Myers G. Cell Detection with Star-Convex Polygons. MICCAI 2018. doi: 10.1007/978-3-030-00934-2_30 + + > Weigert M, Schmidt U, Haase R, Sugawara K, Myers G. Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy. WACV 2020. doi: 10.1109/WACV45572.2020.9093435 + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) diff --git a/README.md b/README.md index d00e4ba9..ceda309c 100644 --- a/README.md +++ b/README.md @@ -31,6 +31,12 @@ the following steps:

+For Visium HD data, cells can optionally replace bins as the analysis unit, +using a cell segmentation from Space Ranger, [Cellpose](https://github.com/MouseLand/cellpose), +[StarDist](https://github.com/stardist/stardist) or a user-supplied file. For +data already processed by Space Ranger, the last three are applied with +[bin2cell](https://github.com/Teichlab/bin2cell). + The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results diff --git a/docs/output.md b/docs/output.md index 9a983a62..5b20f33b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -16,6 +16,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: - [Space Ranger](#space-ranger) +- [Cell segmentation](#cell-segmentation) - [FastQC](#fastqc) - [Per-sample data](#per-sample-data) - [Per-sample reports](#per-sample-reports) @@ -47,6 +48,27 @@ All files produced by Space Ranger are currently published as output of this pipeline, regardless if they're being used downstream or not; you can find more information about these files at the [10X website](https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/overview). +## Cell segmentation + +
+Output files + +- `/segmentation/` + - `*_cp_masks.tif` or `*.stardist.tif`: Label mask from cellpose or stardist, + on the (optionally downscaled) image. + - `*_segmentation.geojson`: Cell polygons in full-resolution image pixels. + +
+ +Only produced with `--segmentation_method cellpose` or `stardist`. Space Ranger +segmentation results are in `/spaceranger/outs/segmented_outputs/`. + +When a segmentation is used, cells replace bins as the analysis unit. The +SpatialData objects (see [Integration](#integration)) then also contain the +bin table as `_bin_table`, and the cell polygons as `_cells` +shapes when bins were grouped with bin2cell (otherwise as read from Space +Ranger's `segmented_outputs/`). + ## FastQC
@@ -123,6 +145,8 @@ selected per sample and ranked by in how many samples they are highly variable. - `merged.zarr`: Merged SpatialData object containing all samples (before integration). - `.zarr`: Integrated SpatialData object with batch-corrected results. + With cell segmentation, both `.zarr` objects also hold each sample's cell + shapes and `_bin_table` table (see [Cell segmentation](#cell-segmentation)). - `.h5ad`: Integrated AnnData object with batch-corrected embeddings and clustering. The PCA of the merged data is in `obsm["X_pca_merged"]`, while `obsm["X_pca"]` holds each spot's coordinates in the PCA of its own diff --git a/docs/usage.md b/docs/usage.md index 2814e30a..5c5d8dfa 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -55,18 +55,19 @@ fluorescence images can be supplied using the `colorizedimage` or `darkimage` co Please refer to the following table for an overview of all supported columns: -| Column | Description | -| ------------------ | -------------------------------------------------------------------------------------------------------------------- | -| `sample` | Unique sample identifier. MUST match the prefix of the fastq files | -| `fastq_dir` | Path to directory where the sample FASTQ files are stored. May be a `.tar` or `.tar.gz` file instead of a directory. | -| `image` | Brightfield microscopy image | -| `cytaimage` | Brightfield tissue image captured with Cytassist device | -| `colorizedimage` | A color composite of one or more fluorescence image channels saved as a single-page, single-file color TIFF or JPEG | -| `darkimage` | Dark background fluorescence microscopy image | -| `slide` | The Visium slide ID used for the sequencing. | -| `area` | Which slide area contains the tissue sample. | -| `manual_alignment` | Path to the manual alignment file (optional) | -| `slidefile` | Slide specification as JSON. Overrides `slide` and `area` if specified. (optional) | +| Column | Description | +| ------------------- | -------------------------------------------------------------------------------------------------------------------- | +| `sample` | Unique sample identifier. MUST match the prefix of the fastq files | +| `fastq_dir` | Path to directory where the sample FASTQ files are stored. May be a `.tar` or `.tar.gz` file instead of a directory. | +| `image` | Brightfield microscopy image | +| `cytaimage` | Brightfield tissue image captured with Cytassist device | +| `colorizedimage` | A color composite of one or more fluorescence image channels saved as a single-page, single-file color TIFF or JPEG | +| `darkimage` | Dark background fluorescence microscopy image | +| `slide` | The Visium slide ID used for the sequencing. | +| `area` | Which slide area contains the tissue sample. | +| `manual_alignment` | Path to the manual alignment file (optional) | +| `slidefile` | Slide specification as JSON. Overrides `slide` and `area` if specified. (optional) | +| `segmentation_file` | Cell segmentation for Visium HD, as GeoJSON or TIFF/NPY label mask, in full-resolution image pixels. (optional) | > [!NOTE] > @@ -108,14 +109,47 @@ SAMPLE_1,outs.tar.gz SAMPLE_2,outs.tar.gz ``` -| Column | Description | -| ----------------- | ----------------------------------------------------------------------------------------- | -| `sample` | Unique sample identifier. | -| `spaceranger_dir` | Output directory generated by spaceranger. May be a `.tar.gz` file instead of a directory | +| Column | Description | +| ------------------- | ---------------------------------------------------------------------------------------------------------------- | +| `sample` | Unique sample identifier. | +| `spaceranger_dir` | Output directory generated by spaceranger. May be a `.tar.gz` file instead of a directory | +| `image` | Full-resolution tissue image, needed for `--segmentation_method cellpose` or `stardist` (optional) | +| `segmentation_file` | Cell segmentation for Visium HD, as GeoJSON or TIFF/NPY label mask, in full-resolution image pixels. (optional) | The Space Ranger output directory is typically called `outs` and contains both gene expression matrices as well as spatial information. +## Cell segmentation (Visium HD) + +By default, Visium HD data is analysed per bin (`--hd_bin_size`). You can +instead group the 2 µm bins into cells. There are two ways, which cannot be +combined: + +- `--segmentation_method`: `spaceranger` uses Space Ranger's own nucleus + segmentation. `cellpose` or `stardist` segment the samplesheet `image`, and + the result is passed to Space Ranger. `stardist` finds nuclei, which Space + Ranger expands by `--segmentation_expansion_distance` microns; `cellpose` + finds whole cells, which are not expanded. +- `segmentation_file` in the samplesheet: a segmentation you computed yourself, + either as GeoJSON (`.geojson` or `.json`) or as a label mask (TIFF or NPY), in + full-resolution image pixels. + +Before `cellpose` or `stardist`, the image is converted to an RGB TIFF and, with +`--segmentation_downscale` above 1, downscaled. Downscaling is faster but detects +far fewer nuclei, so the default is full resolution. `cellpose` uses +Cellpose-SAM, which needs a GPU on full-size Visium HD images; use +`-profile gpu`, or `stardist` if no GPU is available. + +For processed data (`spaceranger_dir`), `spaceranger` reads the segmentation +from the Space Ranger output. The other options group the 2 µm bins with +[bin2cell](https://github.com/Teichlab/bin2cell); `cellpose` and `stardist` +need an `image` column. + +When cells are used, all downstream steps run on cells, and the bin table is +kept in the SpatialData object. Without a segmentation, Space Ranger's nucleus +segmentation is turned off for Visium HD, so `segmented_outputs/` is not +produced. + ## Space Ranger The pipeline exposes several of Space Ranger's parameters when executing with From 16d01c2808716fbf2cdb7e671b620c8a230f8144 Mon Sep 17 00:00:00 2001 From: Christophe Avenel Date: Mon, 12 Oct 2026 03:53:48 +0200 Subject: [PATCH 6/7] Update nf-test snapshots Regenerated with nf-test 0.9.4 and Nextflow 25.10.4, as used in CI. Most changes are tool versions from the updated image. The Visium HD pipeline test no longer lists Space Ranger's segmented_outputs, which is now only produced when cells are requested. New snapshots for IMAGE_DOWNSCALE, MASK_TO_GEOJSON and SDATA_BIN_TO_CELL. --- .../adata/extend/tests/main.nf.test.snap | 242 +- .../local/adata/merge/tests/main.nf.test.snap | 68 +- .../image/downscale/tests/main.nf.test.snap | 35 + .../tests/main.nf.test.snap | 38 +- .../scanpy/filter/tests/main.nf.test.snap | 78 +- .../scanpy/harmony/tests/main.nf.test.snap | 32 +- .../tests/main.nf.test.snap | 116 +- .../scanpy/leiden/tests/main.nf.test.snap | 20 +- .../scanpy/log1p/tests/main.nf.test.snap | 8 +- .../scanpy/neighbors/tests/main.nf.test.snap | 16 +- .../normalize_total/tests/main.nf.test.snap | 8 +- .../local/scanpy/pca/tests/main.nf.test.snap | 38 +- .../rank_genes_groups/tests/main.nf.test.snap | 56 +- .../scanpy/scanorama/tests/main.nf.test.snap | 32 +- .../local/scanpy/umap/tests/main.nf.test.snap | 22 +- .../sdata/bin_to_cell/tests/main.nf.test.snap | 39 + .../local/sdata/merge/tests/main.nf.test.snap | 416 +- .../sdata/read_visium/tests/main.nf.test.snap | 228 +- .../to_legacy_anndata/tests/main.nf.test.snap | 18 +- .../update_table/tests/main.nf.test.snap | 934 ++-- .../mask_to_geojson/tests/main.nf.test.snap | 35 + .../tests/main.nf.test.snap | 26 +- .../nhood_enrichment/tests/main.nf.test.snap | 26 +- .../spatial_autocorr/tests/main.nf.test.snap | 44 +- .../spatial_neighbors/tests/main.nf.test.snap | 44 +- tests/default.nf.test.snap | 1553 +++--- tests/test_downstream.nf.test.snap | 4378 ++++++++--------- tests/test_skip_downstream.nf.test.snap | 238 +- tests/test_spaceranger_ffpe_hd.nf.test.snap | 2361 ++++----- tests/test_spaceranger_ffpe_v1.nf.test.snap | 2288 ++++----- 30 files changed, 6297 insertions(+), 7140 deletions(-) create mode 100644 modules/local/image/downscale/tests/main.nf.test.snap create mode 100644 modules/local/sdata/bin_to_cell/tests/main.nf.test.snap create mode 100644 modules/local/segmentation/mask_to_geojson/tests/main.nf.test.snap diff --git a/modules/local/adata/extend/tests/main.nf.test.snap b/modules/local/adata/extend/tests/main.nf.test.snap index 4a2056ff..02b2c487 100644 --- a/modules/local/adata/extend/tests/main.nf.test.snap +++ b/modules/local/adata/extend/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - pkl - index mismatch reindexed with missing entries": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -16,13 +16,13 @@ "var": { "index": "_index", "columns": [ - "hb", - "mean_counts", + "symbols", "mt", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "symbols", "total_counts" ] }, @@ -46,16 +46,16 @@ ] } ], - "timestamp": "2026-10-07T14:31:27.383207", + "timestamp": "2026-10-12T00:49:26.6561249", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - spatial obsp and uns": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 11397, @@ -63,18 +63,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -105,16 +105,16 @@ ] } ], - "timestamp": "2026-10-04T11:34:43.70328", + "timestamp": "2026-10-12T00:30:54.148960162", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - layers aligned": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 834, @@ -122,41 +122,41 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "mean_counts", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells" ] }, "layers": [ @@ -183,16 +183,16 @@ ] } ], - "timestamp": "2026-10-04T13:26:11.484443", + "timestamp": "2026-10-12T00:51:19.04851725", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - obs and var": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -200,31 +200,31 @@ "obs": { "index": "_index", "columns": [ + "sample", "n_genes_by_counts", - "pct_counts_hb", - "pct_counts_in_top_100_genes", - "pct_counts_in_top_200_genes", + "total_counts", "pct_counts_in_top_500_genes", + "pct_counts_in_top_200_genes", + "pct_counts_in_top_100_genes", "pct_counts_in_top_50_genes", + "total_counts_mt", "pct_counts_mt", + "total_counts_ribo", "pct_counts_ribo", - "sample", - "total_counts", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "pct_counts_hb" ] }, "var": { "index": "_index", "columns": [ - "hb", - "mean_counts", + "symbols", "mt", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "symbols", "total_counts" ] }, @@ -248,16 +248,16 @@ ] } ], - "timestamp": "2026-10-01T20:26:10.99457", + "timestamp": "2026-10-12T00:07:41.185927259", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - obsp and uns": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -296,16 +296,16 @@ ] } ], - "timestamp": "2026-10-01T20:25:47.736926", + "timestamp": "2026-10-12T00:06:39.961708237", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - key collision allowed": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -313,8 +313,8 @@ "obs": { "index": "_index", "columns": [ - "clusters", - "sample" + "sample", + "clusters" ] }, "var": { @@ -346,16 +346,16 @@ ] } ], - "timestamp": "2026-09-30T15:35:02.65551", + "timestamp": "2026-10-12T00:17:33.020582272", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - duplicate names strict": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -363,31 +363,31 @@ "obs": { "index": "_index", "columns": [ + "sample", "n_genes_by_counts", - "pct_counts_hb", - "pct_counts_in_top_100_genes", - "pct_counts_in_top_200_genes", + "total_counts", "pct_counts_in_top_500_genes", + "pct_counts_in_top_200_genes", + "pct_counts_in_top_100_genes", "pct_counts_in_top_50_genes", + "total_counts_mt", "pct_counts_mt", + "total_counts_ribo", "pct_counts_ribo", - "sample", - "total_counts", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "pct_counts_hb" ] }, "var": { "index": "_index", "columns": [ - "hb", - "mean_counts", + "symbols", "mt", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "symbols", "total_counts" ] }, @@ -411,16 +411,16 @@ ] } ], - "timestamp": "2026-10-01T21:10:59.250684", + "timestamp": "2026-10-12T00:50:20.195593324", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - obsm, varm and uns": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -457,16 +457,16 @@ ] } ], - "timestamp": "2026-10-01T07:00:54.87345", + "timestamp": "2026-10-12T00:04:30.845187214", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - uns from several modules": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 11397, @@ -474,19 +474,19 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", "in_tissue", + "array_row", + "array_col", + "spot_id", "region", - "spot_id" + "clusters" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -525,16 +525,16 @@ ] } ], - "timestamp": "2026-10-04T11:37:09.502245", + "timestamp": "2026-10-12T00:42:34.804172326", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - index mismatch reindexed": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 5756, @@ -542,17 +542,17 @@ "obs": { "index": "_index", "columns": [ - "clusters", + "sample", "n_counts", "n_genes", - "sample" + "clusters" ] }, "var": { "index": "_index", "columns": [ - "n_cells", - "symbols" + "symbols", + "n_cells" ] }, "layers": [ @@ -578,16 +578,16 @@ ] } ], - "timestamp": "2026-10-01T20:34:17.527648", + "timestamp": "2026-10-12T00:25:26.036056365", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - pkl - var and uns": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -601,11 +601,11 @@ "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", + "symbols", "highly_variable", "means", - "symbols" + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -629,16 +629,16 @@ ] } ], - "timestamp": "2026-10-01T20:26:29.110654", + "timestamp": "2026-10-12T00:09:21.878197753", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - layers strict": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 11397, @@ -646,18 +646,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -685,10 +685,10 @@ ] } ], - "timestamp": "2026-10-04T11:56:58.096627", + "timestamp": "2026-10-12T00:52:36.814232873", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "stub": { @@ -727,7 +727,7 @@ "homo_sapiens - pkl - obs and uns": { "content": [ [ - "versions.yml:md5,849bbf640638ea746ca197fb83c193a8" + "versions.yml:md5,bc92d0acd4cc763dc7445b12d09a9338" ], { "n_obs": 12940, @@ -735,8 +735,8 @@ "obs": { "index": "_index", "columns": [ - "clusters", - "sample" + "sample", + "clusters" ] }, "var": { @@ -768,10 +768,10 @@ ] } ], - "timestamp": "2026-09-30T15:33:40.149671", + "timestamp": "2026-10-12T00:03:44.688239866", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/adata/merge/tests/main.nf.test.snap b/modules/local/adata/merge/tests/main.nf.test.snap index 476ddc3b..1238b9b0 100644 --- a/modules/local/adata/merge/tests/main.nf.test.snap +++ b/modules/local/adata/merge/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - inner": { "content": [ [ - "versions.yml:md5,000ad1cdc4326c1b33c0fbd3557056f5" + "versions.yml:md5,c4c576f638087d2747ca53e757d5652d" ], { "n_obs": 20313, @@ -10,8 +10,8 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { @@ -40,16 +40,16 @@ ] } ], - "timestamp": "2026-10-01T20:52:45.710987", + "timestamp": "2026-10-12T00:54:03.244702802", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - per-sample var columns": { "content": [ [ - "versions.yml:md5,000ad1cdc4326c1b33c0fbd3557056f5" + "versions.yml:md5,c4c576f638087d2747ca53e757d5652d" ], { "n_obs": 20313, @@ -57,28 +57,28 @@ "obs": { "index": "_index", "columns": [ - "library_id", + "sample", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", - "pct_counts_mt", + "total_counts_ribo", "pct_counts_ribo", - "sample", - "total_counts", "total_counts_hb", + "pct_counts_hb", + "pct_counts_mt", "total_counts_mt", - "total_counts_ribo" + "library_id" ] }, "var": { "index": "_index", "columns": [ - "hb", "mt", - "ribo" + "ribo", + "hb" ] }, "layers": [ @@ -101,10 +101,10 @@ ] } ], - "timestamp": "2026-10-05T12:43:34.384823", + "timestamp": "2026-10-12T00:54:39.639479752", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -133,7 +133,7 @@ "homo_sapiens - zarr - preserve spatial data": { "content": [ [ - "versions.yml:md5,000ad1cdc4326c1b33c0fbd3557056f5" + "versions.yml:md5,c4c576f638087d2747ca53e757d5652d" ], { "n_obs": 22794, @@ -141,19 +141,19 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "library_id", + "array_row", + "array_col", + "spot_id", "region", - "spot_id" + "library_id" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -177,16 +177,16 @@ ] } ], - "timestamp": "2026-10-05T12:43:57.018024", + "timestamp": "2026-10-12T00:55:02.586410158", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - outer": { "content": [ [ - "versions.yml:md5,000ad1cdc4326c1b33c0fbd3557056f5" + "versions.yml:md5,c4c576f638087d2747ca53e757d5652d" ], { "n_obs": 20313, @@ -194,8 +194,8 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { @@ -224,10 +224,10 @@ ] } ], - "timestamp": "2026-10-01T20:52:54.856983", + "timestamp": "2026-10-12T00:54:12.445330999", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/image/downscale/tests/main.nf.test.snap b/modules/local/image/downscale/tests/main.nf.test.snap new file mode 100644 index 00000000..1505f64b --- /dev/null +++ b/modules/local/image/downscale/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "homo_sapiens - tif - stub": { + "content": [ + { + "0": [ + [ + { + "id": "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2" + }, + "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_downscaled.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "image": [ + [ + { + "id": "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2" + }, + "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_downscaled.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + } + ], + "timestamp": "2026-10-11T23:50:20.227726524", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/local/scanpy/calculate_qc_metrics/tests/main.nf.test.snap b/modules/local/scanpy/calculate_qc_metrics/tests/main.nf.test.snap index 64b99a91..c2bbac1c 100644 --- a/modules/local/scanpy/calculate_qc_metrics/tests/main.nf.test.snap +++ b/modules/local/scanpy/calculate_qc_metrics/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,6f4b87dd8d7574d03eb384519a2f6283" + "versions.yml:md5,ae0dfc6de67e20dbfeacd9348d091fa0" ], [ "qc_metrics.pkl" @@ -11,16 +11,16 @@ "qc_metrics.pkl" ] ], - "timestamp": "2026-10-01T16:02:28.6669", + "timestamp": "2026-10-12T00:56:26.512106877", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,6f4b87dd8d7574d03eb384519a2f6283" + "versions.yml:md5,ae0dfc6de67e20dbfeacd9348d091fa0" ], { "n_obs": 12940, @@ -28,31 +28,31 @@ "obs": { "index": "_index", "columns": [ + "sample", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", - "pct_counts_mt", + "total_counts_ribo", "pct_counts_ribo", - "sample", - "total_counts", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "pct_counts_hb", + "pct_counts_mt", + "total_counts_mt" ] }, "var": { "index": "_index", "columns": [ - "hb", - "mean_counts", + "symbols", "mt", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "symbols", "total_counts" ] }, @@ -82,10 +82,10 @@ "qc_metrics.pkl" ] ], - "timestamp": "2026-10-01T16:02:08.757028", + "timestamp": "2026-10-12T00:56:03.06505058", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { diff --git a/modules/local/scanpy/filter/tests/main.nf.test.snap b/modules/local/scanpy/filter/tests/main.nf.test.snap index d4bb9612..91fdbd74 100644 --- a/modules/local/scanpy/filter/tests/main.nf.test.snap +++ b/modules/local/scanpy/filter/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,b6a994de579a3ecaab530e42ab0b9d2d" + "versions.yml:md5,b29221f3456acc092c52c963c78d6959" ], { "n_obs": 9, @@ -10,35 +10,35 @@ "obs": { "index": "_index", "columns": [ - "n_counts", - "n_genes", + "sample", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", - "pct_counts_mt", + "total_counts_ribo", "pct_counts_ribo", - "sample", - "total_counts", "total_counts_hb", + "pct_counts_hb", + "pct_counts_mt", "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes" ] }, "var": { "index": "_index", "columns": [ - "hb", - "mean_counts", + "symbols", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "symbols", - "total_counts" + "total_counts", + "n_cells" ] }, "layers": [ @@ -69,10 +69,10 @@ ] ] ], - "timestamp": "2026-10-01T16:31:33.901613", + "timestamp": "2026-10-12T00:57:02.360368299", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -127,7 +127,7 @@ "homo_sapiens - h5ad - with spatial data": { "content": [ [ - "versions.yml:md5,b6a994de579a3ecaab530e42ab0b9d2d" + "versions.yml:md5,b29221f3456acc092c52c963c78d6959" ], { "n_obs": 6583, @@ -135,41 +135,41 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "mean_counts", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells" ] }, "layers": [ @@ -204,10 +204,10 @@ ] ] ], - "timestamp": "2026-10-04T11:18:50.742868", + "timestamp": "2026-10-12T00:58:39.129794874", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/harmony/tests/main.nf.test.snap b/modules/local/scanpy/harmony/tests/main.nf.test.snap index e5042d38..66131248 100644 --- a/modules/local/scanpy/harmony/tests/main.nf.test.snap +++ b/modules/local/scanpy/harmony/tests/main.nf.test.snap @@ -2,22 +2,22 @@ "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,03172681ef9c2e21eed9e9ed573cf597" + "versions.yml:md5,1a0cc1e96a8a9226ad79a52aa779d002" ], [ "X_harmony.pkl" ] ], - "timestamp": "2026-10-01T14:29:06.427218", + "timestamp": "2026-10-12T01:02:02.884191085", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,03172681ef9c2e21eed9e9ed573cf597" + "versions.yml:md5,1a0cc1e96a8a9226ad79a52aa779d002" ], { "n_obs": 20313, @@ -25,8 +25,8 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { @@ -59,10 +59,10 @@ "X_harmony.pkl" ] ], - "timestamp": "2026-10-01T23:01:44.415676", + "timestamp": "2026-10-12T00:59:16.415872338", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -117,7 +117,7 @@ "homo_sapiens - h5ad - custom basis": { "content": [ [ - "versions.yml:md5,03172681ef9c2e21eed9e9ed573cf597" + "versions.yml:md5,1a0cc1e96a8a9226ad79a52aa779d002" ], { "n_obs": 20313, @@ -125,8 +125,8 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { @@ -159,10 +159,10 @@ "X_harmony.pkl" ] ], - "timestamp": "2026-10-05T14:29:32.331045", + "timestamp": "2026-10-12T01:00:55.342232397", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/highly_variable_genes/tests/main.nf.test.snap b/modules/local/scanpy/highly_variable_genes/tests/main.nf.test.snap index e1329b8a..d0fa4046 100644 --- a/modules/local/scanpy/highly_variable_genes/tests/main.nf.test.snap +++ b/modules/local/scanpy/highly_variable_genes/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - seurat flavor - no h5ad output": { "content": [ [ - "versions.yml:md5,e13181af4757604b85af5368250a94d7" + "versions.yml:md5,4075c956526cd896fb9b53c6d3c2c90f" ], [ "highly_variable_genes.pkl" @@ -11,16 +11,16 @@ "hvg.pkl" ] ], - "timestamp": "2026-10-02T11:54:27.144755", + "timestamp": "2026-10-12T01:05:36.583229933", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - cell_ranger flavor": { "content": [ [ - "versions.yml:md5,e13181af4757604b85af5368250a94d7" + "versions.yml:md5,4075c956526cd896fb9b53c6d3c2c90f" ], { "n_obs": 12940, @@ -28,39 +28,39 @@ "obs": { "index": "_index", "columns": [ - "n_counts", - "n_genes", + "sample", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", - "pct_counts_mt", + "total_counts_ribo", "pct_counts_ribo", - "sample", - "total_counts", "total_counts_hb", + "pct_counts_hb", + "pct_counts_mt", "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "hb", - "highly_variable", - "mean_counts", - "means", + "symbols", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "symbols", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -90,16 +90,16 @@ "hvg.pkl" ] ], - "timestamp": "2026-10-02T11:37:06.12832", + "timestamp": "2026-10-12T01:06:27.98309696", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - fallback with too few genes - batch key": { "content": [ [ - "versions.yml:md5,e13181af4757604b85af5368250a94d7" + "versions.yml:md5,4075c956526cd896fb9b53c6d3c2c90f" ], { "n_obs": 20313, @@ -107,19 +107,19 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { "index": "_index", "columns": [ + "highly_variable", + "means", "dispersions", "dispersions_norm", - "highly_variable", - "highly_variable_intersection", "highly_variable_nbatches", - "means" + "highly_variable_intersection" ] }, "layers": [ @@ -149,10 +149,10 @@ "hvg.pkl" ] ], - "timestamp": "2026-10-05T14:03:04.83762", + "timestamp": "2026-10-12T01:07:40.104981379", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -223,7 +223,7 @@ "homo_sapiens - h5ad - seurat flavor - batch key": { "content": [ [ - "versions.yml:md5,e13181af4757604b85af5368250a94d7" + "versions.yml:md5,4075c956526cd896fb9b53c6d3c2c90f" ], { "n_obs": 20313, @@ -231,19 +231,19 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { "index": "_index", "columns": [ + "highly_variable", + "means", "dispersions", "dispersions_norm", - "highly_variable", - "highly_variable_intersection", "highly_variable_nbatches", - "means" + "highly_variable_intersection" ] }, "layers": [ @@ -273,16 +273,16 @@ "hvg.pkl" ] ], - "timestamp": "2026-10-05T14:02:48.191739", + "timestamp": "2026-10-12T01:07:18.147411489", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - fallback with too few genes": { "content": [ [ - "versions.yml:md5,e13181af4757604b85af5368250a94d7" + "versions.yml:md5,4075c956526cd896fb9b53c6d3c2c90f" ], { "n_obs": 12940, @@ -296,11 +296,11 @@ "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", + "symbols", "highly_variable", "means", - "symbols" + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -330,16 +330,16 @@ "hvg.pkl" ] ], - "timestamp": "2026-10-02T11:18:06.439336", + "timestamp": "2026-10-12T01:06:45.972906019", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - seurat flavor": { "content": [ [ - "versions.yml:md5,e13181af4757604b85af5368250a94d7" + "versions.yml:md5,4075c956526cd896fb9b53c6d3c2c90f" ], { "n_obs": 12940, @@ -353,11 +353,11 @@ "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", + "symbols", "highly_variable", "means", - "symbols" + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -387,10 +387,10 @@ "hvg.pkl" ] ], - "timestamp": "2026-10-01T23:02:55.350186", + "timestamp": "2026-10-12T01:05:16.652597012", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/leiden/tests/main.nf.test.snap b/modules/local/scanpy/leiden/tests/main.nf.test.snap index 98139d25..825761cb 100644 --- a/modules/local/scanpy/leiden/tests/main.nf.test.snap +++ b/modules/local/scanpy/leiden/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,310276833f0e291b5c85bb9b866b80bd" + "versions.yml:md5,6624dea8daa1fefbf2c7ed2da603f826" ], { "n_obs": 12940, @@ -10,8 +10,8 @@ "obs": { "index": "_index", "columns": [ - "clusters", - "sample" + "sample", + "clusters" ] }, "var": { @@ -49,10 +49,10 @@ "clusters.pkl" ] ], - "timestamp": "2026-09-29T08:50:43.231158", + "timestamp": "2026-10-12T01:09:09.38601527", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -123,7 +123,7 @@ "homo_sapiens - no h5ad": { "content": [ [ - "versions.yml:md5,310276833f0e291b5c85bb9b866b80bd" + "versions.yml:md5,6624dea8daa1fefbf2c7ed2da603f826" ], [ "clusters.pkl" @@ -132,10 +132,10 @@ "clusters.pkl" ] ], - "timestamp": "2026-09-29T08:48:42.759554", + "timestamp": "2026-10-12T01:10:10.89421561", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/log1p/tests/main.nf.test.snap b/modules/local/scanpy/log1p/tests/main.nf.test.snap index b453d002..86d8e18f 100644 --- a/modules/local/scanpy/log1p/tests/main.nf.test.snap +++ b/modules/local/scanpy/log1p/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,f534d0e930e0356dc8d91ac5935ce2a4" + "versions.yml:md5,9ae8ef5a475cc6180e56364f0ad58027" ], { "n_obs": 12940, @@ -39,10 +39,10 @@ ] } ], - "timestamp": "2026-10-01T19:06:12.129025", + "timestamp": "2026-10-12T01:10:32.518525618", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { diff --git a/modules/local/scanpy/neighbors/tests/main.nf.test.snap b/modules/local/scanpy/neighbors/tests/main.nf.test.snap index ec8b8939..ffebbd29 100644 --- a/modules/local/scanpy/neighbors/tests/main.nf.test.snap +++ b/modules/local/scanpy/neighbors/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,3ed02ce5d9eb07b2e974b8d7b80e7c8d" + "versions.yml:md5,1a555766cefab5c0e9d874b438da499a" ], [ "connectivities.pkl", @@ -12,10 +12,10 @@ "neighbors.pkl" ] ], - "timestamp": "2026-10-01T13:58:01.71553", + "timestamp": "2026-10-12T01:12:29.590426096", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -92,7 +92,7 @@ "homo_sapiens - h5ad - with pca": { "content": [ [ - "versions.yml:md5,3ed02ce5d9eb07b2e974b8d7b80e7c8d" + "versions.yml:md5,1a555766cefab5c0e9d874b438da499a" ], { "n_obs": 12940, @@ -138,10 +138,10 @@ "neighbors.pkl" ] ], - "timestamp": "2026-10-01T13:57:24.349215", + "timestamp": "2026-10-12T01:11:34.481115584", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/normalize_total/tests/main.nf.test.snap b/modules/local/scanpy/normalize_total/tests/main.nf.test.snap index 97d09efd..9dc31a74 100644 --- a/modules/local/scanpy/normalize_total/tests/main.nf.test.snap +++ b/modules/local/scanpy/normalize_total/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,76284d81803fab43f0ae80b07e38f742" + "versions.yml:md5,5a94098e683e45c34680e2ad39b9dfbc" ], { "n_obs": 12940, @@ -39,10 +39,10 @@ ] } ], - "timestamp": "2026-10-01T19:05:36.438111", + "timestamp": "2026-10-12T01:13:16.892320242", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { diff --git a/modules/local/scanpy/pca/tests/main.nf.test.snap b/modules/local/scanpy/pca/tests/main.nf.test.snap index 35e9ccac..45544940 100644 --- a/modules/local/scanpy/pca/tests/main.nf.test.snap +++ b/modules/local/scanpy/pca/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - with highly variable genes": { "content": [ [ - "versions.yml:md5,72a45b1aedaf9f2f5dcedffc73b2a79b" + "versions.yml:md5,dcf3576afc6638b4e8f70208d428940b" ], { "n_obs": 12940, @@ -16,11 +16,11 @@ "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", + "symbols", "highly_variable", "means", - "symbols" + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -54,16 +54,16 @@ "pca.pkl" ] ], - "timestamp": "2026-10-01T23:07:35.4818", + "timestamp": "2026-10-12T01:13:49.788069575", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,72a45b1aedaf9f2f5dcedffc73b2a79b" + "versions.yml:md5,dcf3576afc6638b4e8f70208d428940b" ], [ "X_pca.pkl" @@ -75,16 +75,16 @@ "pca.pkl" ] ], - "timestamp": "2026-09-30T14:58:26.136705", + "timestamp": "2026-10-12T01:14:29.348481016", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,72a45b1aedaf9f2f5dcedffc73b2a79b" + "versions.yml:md5,dcf3576afc6638b4e8f70208d428940b" ], { "n_obs": 12940, @@ -130,10 +130,10 @@ "pca.pkl" ] ], - "timestamp": "2026-09-30T14:58:16.320895", + "timestamp": "2026-10-12T01:14:03.643829975", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -220,7 +220,7 @@ "homo_sapiens - h5ad - custom key": { "content": [ [ - "versions.yml:md5,72a45b1aedaf9f2f5dcedffc73b2a79b" + "versions.yml:md5,dcf3576afc6638b4e8f70208d428940b" ], { "n_obs": 12940, @@ -266,10 +266,10 @@ "X_pca_merged.pkl" ] ], - "timestamp": "2026-10-05T14:24:15.770266", + "timestamp": "2026-10-12T01:14:16.928495752", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/rank_genes_groups/tests/main.nf.test.snap b/modules/local/scanpy/rank_genes_groups/tests/main.nf.test.snap index 99540cd5..a005b63b 100644 --- a/modules/local/scanpy/rank_genes_groups/tests/main.nf.test.snap +++ b/modules/local/scanpy/rank_genes_groups/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - wilcoxon": { "content": [ [ - "versions.yml:md5,5cd8bc30e81999f69e36ed1b0d89b970" + "versions.yml:md5,00f6eb8e04107d1fe9a35ba21fc75e70" ], { "n_obs": 12940, @@ -10,8 +10,8 @@ "obs": { "index": "_index", "columns": [ - "clusters", - "sample" + "sample", + "clusters" ] }, "var": { @@ -47,16 +47,16 @@ "rank_genes_groups.pkl" ] ], - "timestamp": "2026-10-01T15:24:25.835022", + "timestamp": "2026-10-12T01:16:11.091588252", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - logreg": { "content": [ [ - "versions.yml:md5,5cd8bc30e81999f69e36ed1b0d89b970" + "versions.yml:md5,00f6eb8e04107d1fe9a35ba21fc75e70" ], { "n_obs": 12940, @@ -64,8 +64,8 @@ "obs": { "index": "_index", "columns": [ - "clusters", - "sample" + "sample", + "clusters" ] }, "var": { @@ -101,25 +101,25 @@ "rank_genes_groups.pkl" ] ], - "timestamp": "2026-10-01T15:27:37.270096", + "timestamp": "2026-10-12T01:20:59.559521159", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - wilcoxon - no h5ad output": { "content": [ [ - "versions.yml:md5,5cd8bc30e81999f69e36ed1b0d89b970" + "versions.yml:md5,00f6eb8e04107d1fe9a35ba21fc75e70" ], [ "rank_genes_groups.pkl" ] ], - "timestamp": "2026-10-01T15:25:16.709227", + "timestamp": "2026-10-12T01:17:31.489361505", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -174,7 +174,7 @@ "homo_sapiens - h5ad - t-test_overstim_var": { "content": [ [ - "versions.yml:md5,5cd8bc30e81999f69e36ed1b0d89b970" + "versions.yml:md5,00f6eb8e04107d1fe9a35ba21fc75e70" ], { "n_obs": 12940, @@ -182,8 +182,8 @@ "obs": { "index": "_index", "columns": [ - "clusters", - "sample" + "sample", + "clusters" ] }, "var": { @@ -219,16 +219,16 @@ "rank_genes_groups.pkl" ] ], - "timestamp": "2026-10-01T15:26:50.539956", + "timestamp": "2026-10-12T01:19:52.863926012", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - t-test": { "content": [ [ - "versions.yml:md5,5cd8bc30e81999f69e36ed1b0d89b970" + "versions.yml:md5,00f6eb8e04107d1fe9a35ba21fc75e70" ], { "n_obs": 12940, @@ -236,8 +236,8 @@ "obs": { "index": "_index", "columns": [ - "clusters", - "sample" + "sample", + "clusters" ] }, "var": { @@ -273,10 +273,10 @@ "rank_genes_groups.pkl" ] ], - "timestamp": "2026-10-01T15:26:03.572618", + "timestamp": "2026-10-12T01:18:41.296120649", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/scanorama/tests/main.nf.test.snap b/modules/local/scanpy/scanorama/tests/main.nf.test.snap index 60f6d219..303303ee 100644 --- a/modules/local/scanpy/scanorama/tests/main.nf.test.snap +++ b/modules/local/scanpy/scanorama/tests/main.nf.test.snap @@ -2,22 +2,22 @@ "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,e38ec89768de8bf84a68a506577d0e4e" + "versions.yml:md5,44757daff0e1ec8dedc7f16ef2840999" ], [ "X_scanorama.pkl" ] ], - "timestamp": "2026-10-01T14:34:09.345792", + "timestamp": "2026-10-12T01:22:56.782619556", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,e38ec89768de8bf84a68a506577d0e4e" + "versions.yml:md5,44757daff0e1ec8dedc7f16ef2840999" ], { "n_obs": 20313, @@ -25,8 +25,8 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { @@ -59,10 +59,10 @@ "X_scanorama.pkl" ] ], - "timestamp": "2026-10-01T23:12:58.078708", + "timestamp": "2026-10-12T01:21:51.468596498", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -117,7 +117,7 @@ "homo_sapiens - h5ad - custom basis": { "content": [ [ - "versions.yml:md5,e38ec89768de8bf84a68a506577d0e4e" + "versions.yml:md5,44757daff0e1ec8dedc7f16ef2840999" ], { "n_obs": 20313, @@ -125,8 +125,8 @@ "obs": { "index": "_index", "columns": [ - "library_id", - "sample" + "sample", + "library_id" ] }, "var": { @@ -159,10 +159,10 @@ "X_scanorama.pkl" ] ], - "timestamp": "2026-10-05T14:31:15.226799", + "timestamp": "2026-10-12T01:22:23.03318494", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/local/scanpy/umap/tests/main.nf.test.snap b/modules/local/scanpy/umap/tests/main.nf.test.snap index 57ab4e89..9bb8ff1e 100644 --- a/modules/local/scanpy/umap/tests/main.nf.test.snap +++ b/modules/local/scanpy/umap/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,644846add945175d74eb0fce068a0241" + "versions.yml:md5,4ddc957bdbade42c2221d69c10d318f3" ], [ "X_umap.pkl" @@ -11,16 +11,16 @@ "X_umap.pkl" ] ], - "timestamp": "2026-10-01T14:26:48.447133", + "timestamp": "2026-10-12T01:26:34.697715121", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,644846add945175d74eb0fce068a0241" + "versions.yml:md5,4ddc957bdbade42c2221d69c10d318f3" ], { "n_obs": 12940, @@ -34,11 +34,11 @@ "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", + "symbols", "highly_variable", "means", - "symbols" + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -73,10 +73,10 @@ "X_umap.pkl" ] ], - "timestamp": "2026-10-01T23:14:55.987667", + "timestamp": "2026-10-12T01:25:04.927287453", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { diff --git a/modules/local/sdata/bin_to_cell/tests/main.nf.test.snap b/modules/local/sdata/bin_to_cell/tests/main.nf.test.snap new file mode 100644 index 00000000..55e20999 --- /dev/null +++ b/modules/local/sdata/bin_to_cell/tests/main.nf.test.snap @@ -0,0 +1,39 @@ +{ + "homo_sapiens - zarr - stub": { + "content": [ + { + "0": [ + [ + { + "id": "CytAssist_11mm_FFPE_Human_Glioblastoma_2" + }, + [ + ".zgroup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "sdata": [ + [ + { + "id": "CytAssist_11mm_FFPE_Human_Glioblastoma_2" + }, + [ + ".zgroup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + } + ], + "timestamp": "2026-10-12T01:26:56.766707629", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/local/sdata/merge/tests/main.nf.test.snap b/modules/local/sdata/merge/tests/main.nf.test.snap index 58323fef..666c51fc 100644 --- a/modules/local/sdata/merge/tests/main.nf.test.snap +++ 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b/modules/local/segmentation/mask_to_geojson/tests/main.nf.test.snap new file mode 100644 index 00000000..c552ec48 --- /dev/null +++ b/modules/local/segmentation/mask_to_geojson/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "homo_sapiens - tif - stub": { + "content": [ + { + "0": [ + [ + { + "id": "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2" + }, + "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_segmentation.geojson:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "geojson": [ + [ + { + "id": "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2" + }, + "Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2_segmentation.geojson:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + } + ], + "timestamp": "2026-10-12T01:29:53.198173342", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/local/squidpy/interaction_matrix/tests/main.nf.test.snap b/modules/local/squidpy/interaction_matrix/tests/main.nf.test.snap index 53309b29..2f81b67d 100644 --- a/modules/local/squidpy/interaction_matrix/tests/main.nf.test.snap +++ b/modules/local/squidpy/interaction_matrix/tests/main.nf.test.snap @@ -2,22 +2,22 @@ "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,78677e1663cf16b9059e86c4765cfd1f" + "versions.yml:md5,bae4f2ea2da20da88957463e51503d3f" ], [ "clusters_interactions.pkl" ] ], - "timestamp": "2026-10-01T15:38:47.838736", + "timestamp": "2026-10-12T03:25:57.220284803", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,78677e1663cf16b9059e86c4765cfd1f" + "versions.yml:md5,bae4f2ea2da20da88957463e51503d3f" ], { "n_obs": 11397, @@ -25,19 +25,19 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", "in_tissue", + "array_row", + "array_col", + "spot_id", "region", - "spot_id" + "clusters" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -77,10 +77,10 @@ "clusters_interactions.pkl" ] ], - "timestamp": "2026-10-04T22:14:23.189904", + "timestamp": "2026-10-12T01:31:29.095343887", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { diff --git a/modules/local/squidpy/nhood_enrichment/tests/main.nf.test.snap b/modules/local/squidpy/nhood_enrichment/tests/main.nf.test.snap index 0463aef3..d6a3190d 100644 --- a/modules/local/squidpy/nhood_enrichment/tests/main.nf.test.snap +++ b/modules/local/squidpy/nhood_enrichment/tests/main.nf.test.snap @@ -2,22 +2,22 @@ "homo_sapiens - h5ad - no h5ad output": { "content": [ [ - "versions.yml:md5,3a9dec789188d5283280cd9de9897f53" + "versions.yml:md5,0775c12444a0f80695bc1931104a1de3" ], [ "clusters_nhood_enrichment.pkl" ] ], - "timestamp": "2026-10-01T15:33:37.347727", + "timestamp": "2026-10-12T03:47:59.186454197", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad": { "content": [ [ - "versions.yml:md5,3a9dec789188d5283280cd9de9897f53" + "versions.yml:md5,0775c12444a0f80695bc1931104a1de3" ], { "n_obs": 11397, @@ -25,19 +25,19 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", "in_tissue", + "array_row", + "array_col", + "spot_id", "region", - "spot_id" + "clusters" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -77,10 +77,10 @@ "clusters_nhood_enrichment.pkl" ] ], - "timestamp": "2026-10-04T22:18:20.210211", + "timestamp": "2026-10-12T01:43:21.064842951", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { diff --git a/modules/local/squidpy/spatial_autocorr/tests/main.nf.test.snap b/modules/local/squidpy/spatial_autocorr/tests/main.nf.test.snap index 524617ca..cc069efd 100644 --- a/modules/local/squidpy/spatial_autocorr/tests/main.nf.test.snap +++ b/modules/local/squidpy/spatial_autocorr/tests/main.nf.test.snap @@ -2,22 +2,22 @@ "homo_sapiens - h5ad - moran - no h5ad output": { "content": [ [ - "versions.yml:md5,47a9ced7fad317df79a0be23f28c3642" + "versions.yml:md5,1620342da065cb8202d2e5f968618fcb" ], [ "moranI.pkl" ] ], - "timestamp": "2026-10-01T15:43:23.496067", + "timestamp": "2026-10-12T03:49:54.518189777", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - moran": { "content": [ [ - "versions.yml:md5,47a9ced7fad317df79a0be23f28c3642" + "versions.yml:md5,1620342da065cb8202d2e5f968618fcb" ], { "n_obs": 11397, @@ -25,18 +25,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -70,16 +70,16 @@ "moranI.pkl" ] ], - "timestamp": "2026-10-04T22:21:47.131605", + "timestamp": "2026-10-12T01:44:52.397039604", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - geary": { "content": [ [ - "versions.yml:md5,47a9ced7fad317df79a0be23f28c3642" + "versions.yml:md5,1620342da065cb8202d2e5f968618fcb" ], { "n_obs": 11397, @@ -87,18 +87,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -132,10 +132,10 @@ "gearyC.pkl" ] ], - "timestamp": "2026-10-04T22:23:44.606833", + "timestamp": "2026-10-12T01:45:51.308161682", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { diff --git a/modules/local/squidpy/spatial_neighbors/tests/main.nf.test.snap b/modules/local/squidpy/spatial_neighbors/tests/main.nf.test.snap index 6e06e19c..849e8f2e 100644 --- a/modules/local/squidpy/spatial_neighbors/tests/main.nf.test.snap +++ b/modules/local/squidpy/spatial_neighbors/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - h5ad - generic": { "content": [ [ - "versions.yml:md5,1af8ea16ef6f0a48c58bca6f26a978a0" + "versions.yml:md5,65150940d4209522a492c8a86ca93d71" ], { "n_obs": 11397, @@ -10,18 +10,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -58,10 +58,10 @@ "spatial_neighbors.pkl" ] ], - "timestamp": "2026-10-04T22:27:13.371062", + "timestamp": "2026-10-12T01:47:20.582039533", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - stub": { @@ -138,7 +138,7 @@ "homo_sapiens - h5ad - grid - no h5ad output": { "content": [ [ - "versions.yml:md5,1af8ea16ef6f0a48c58bca6f26a978a0" + "versions.yml:md5,65150940d4209522a492c8a86ca93d71" ], [ "spatial_connectivities.pkl", @@ -148,16 +148,16 @@ "spatial_neighbors.pkl" ] ], - "timestamp": "2026-10-01T15:21:15.582661", + "timestamp": "2026-10-12T03:52:44.626206322", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - h5ad - grid": { "content": [ [ - "versions.yml:md5,1af8ea16ef6f0a48c58bca6f26a978a0" + "versions.yml:md5,65150940d4209522a492c8a86ca93d71" ], { "n_obs": 11397, @@ -165,18 +165,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -213,10 +213,10 @@ "spatial_neighbors.pkl" ] ], - "timestamp": "2026-10-04T22:25:45.913057", + "timestamp": "2026-10-12T01:46:41.056741186", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 9778655f..b0ba648e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -4,119 +4,119 @@ 36, { "ADATA_EXTEND": { - "anndata": "0.12.4", - "numpy": "2.3.4", - "pandas": "2.3.3", - "python": "3.12.12" + "anndata": "0.13.3.post0", + "numpy": "2.5.3", + "pandas": "3.0.5", + "python": "3.14.7" }, "ADATA_MERGE": { - "anndata": "0.12.4", - "python": "3.12.12" + "anndata": "0.13.3.post0", + 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"integration/data/merged.zarr/tables/CytAssist_11mm_FFPE_Human_Glioblastoma_2_table/zarr.json", + "integration/data/merged.zarr/tables/zarr.json", + "integration/data/merged.zarr/zarr.json" ], [ - "report.yml:md5,b37ad57697e27be7b6f472ae15d0d806", + "report.yml:md5,8cf19d13faf9f25d4ce280c9cee5343e", "clusters.csv:md5,a53b18e9472bb24749d69145d0d3ed9c", "clusters.csv:md5,e61073c0502c14030d7a487f7ef36a20", "clusters.csv:md5,418fd1185ecf9aca9749c1d189373425", @@ -1411,18 +1370,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -1458,46 +1417,46 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", "in_tissue", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -1548,50 +1507,50 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", - "clusters_harmony", "in_tissue", - "library_id", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters", + "library_id", + "clusters_harmony" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "highly_variable_intersection", - "highly_variable_nbatches", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm", + "highly_variable_nbatches", + "highly_variable_intersection" ] }, "layers": [ @@ -1629,10 +1588,10 @@ } ] ], - "timestamp": "2026-10-05T15:32:56.015651204", + "timestamp": "2026-11-06T17:39:57.079276477", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/tests/test_downstream.nf.test.snap b/tests/test_downstream.nf.test.snap index f29e8fa7..0dbcc223 100644 --- a/tests/test_downstream.nf.test.snap +++ b/tests/test_downstream.nf.test.snap @@ -4,139 +4,139 @@ 54, { "ADATA_EXTEND": { - "anndata": "0.12.4", - "numpy": "2.3.4", - "pandas": "2.3.3", - "python": "3.12.12" + "anndata": "0.13.3.post0", + "numpy": "2.5.3", + "pandas": "3.0.5", + "python": "3.14.7" }, "ADATA_MERGE": { - "anndata": "0.12.4", - "python": "3.12.12" + "anndata": "0.13.3.post0", + "python": "3.14.7" }, "REPORT": { - 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"report-integrated.yml:md5,a4d0e2a88b83c3c5035ab9570430991e", "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "multiqc_quality_controls.txt:md5,7d0a51fc23fbc8dfc09aa01f9ac7bbb3" @@ -3167,18 +2845,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -3214,18 +2892,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -3261,46 +2939,46 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", "in_tissue", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -3351,46 +3029,46 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", "in_tissue", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -3441,50 +3119,50 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", - "clusters_harmony", "in_tissue", - "library_id", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters", + "library_id", + "clusters_harmony" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "highly_variable_intersection", - "highly_variable_nbatches", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm", + "highly_variable_nbatches", + "highly_variable_intersection" ] }, "layers": [ @@ -3522,10 +3200,10 @@ } ] ], - "timestamp": "2026-10-05T15:24:16.102537258", + "timestamp": "2026-11-06T17:45:41.437406604", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/tests/test_skip_downstream.nf.test.snap b/tests/test_skip_downstream.nf.test.snap index 05ba89e8..f4b281e0 100644 --- a/tests/test_skip_downstream.nf.test.snap +++ b/tests/test_skip_downstream.nf.test.snap @@ -7,13 +7,13 @@ "fastqc": "0.12.1" }, "SDATA_MERGE": { - "python": "3.12.12", - "spatialdata": "0.5.0" + "python": "3.14.7", + "spatialdata": "0.8.0" }, "SDATA_READ_VISIUM": { - 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"total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -2210,50 +1907,50 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", - "clusters_harmony", "in_tissue", - "library_id", + "array_row", + "array_col", "location_id", - "n_counts", - "n_genes", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters", + "library_id", + "clusters_harmony" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "highly_variable_intersection", - "highly_variable_nbatches", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm", + "highly_variable_nbatches", + "highly_variable_intersection" ] }, "layers": [ @@ -2291,10 +1988,10 @@ } ] ], - "timestamp": "2026-10-05T18:00:46.007301547", + "timestamp": "2026-11-06T18:24:10.511949586", "meta": { - "nf-test": 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"clusters.csv:md5,670c096a5bb6e2ee785305756bfb6134", "clusters.csv:md5,48a27dd2731f0a9456036d2e06fc529e", "clusters.csv:md5,3e61308a892fa5ad93ced13aeda3bbdb", @@ -1826,18 +1674,18 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", "in_tissue", - "region", - "spot_id" + "array_row", + "array_col", + "spot_id", + "region" ] }, "var": { "index": "_index", "columns": [ - "feature_types", "gene_ids", + "feature_types", "genome" ] }, @@ -1873,46 +1721,46 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", "in_tissue", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm" ] }, "layers": [ @@ -1963,50 +1811,50 @@ "obs": { "index": "_index", "columns": [ - "array_col", - "array_row", - "clusters", - "clusters_harmony", "in_tissue", - "library_id", - "n_counts", - "n_genes", + "array_row", + "array_col", + "spot_id", + "region", "n_genes_by_counts", - "pct_counts_hb", + "total_counts", + "pct_counts_in_top_50_genes", "pct_counts_in_top_100_genes", "pct_counts_in_top_200_genes", "pct_counts_in_top_500_genes", - "pct_counts_in_top_50_genes", "pct_counts_mt", + "total_counts_mt", "pct_counts_ribo", - "region", - "spot_id", - "total_counts", + "total_counts_ribo", + "pct_counts_hb", "total_counts_hb", - "total_counts_mt", - "total_counts_ribo" + "n_counts", + "n_genes", + "clusters", + "library_id", + "clusters_harmony" ] }, "var": { "index": "_index", "columns": [ - "dispersions", - "dispersions_norm", - "feature_types", "gene_ids", + "feature_types", "genome", - "hb", - "highly_variable", - "highly_variable_intersection", - "highly_variable_nbatches", - "mean_counts", - "means", "mt", - "n_cells", + "ribo", + "hb", "n_cells_by_counts", + "mean_counts", "pct_dropout_by_counts", - "ribo", - "total_counts" + "total_counts", + "n_cells", + "highly_variable", + "means", + "dispersions", + "dispersions_norm", + "highly_variable_nbatches", + "highly_variable_intersection" ] }, "layers": [ @@ -2044,10 +1892,10 @@ } ] ], - "timestamp": "2026-10-05T15:31:21.226408734", + "timestamp": "2026-11-06T18:34:29.483307191", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file From f2a6d1a846fa5db8218a13f8a74f189d120fcf76 Mon Sep 17 00:00:00 2001 From: cavenel Date: Fri, 6 Nov 2026 20:14:38 +0100 Subject: [PATCH 7/7] Fix table formatting in usage docs --- docs/usage.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 5c5d8dfa..6b387bcb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -109,12 +109,12 @@ SAMPLE_1,outs.tar.gz SAMPLE_2,outs.tar.gz ``` -| Column | Description | -| ------------------- | ---------------------------------------------------------------------------------------------------------------- | -| `sample` | Unique sample identifier. | -| `spaceranger_dir` | Output directory generated by spaceranger. May be a `.tar.gz` file instead of a directory | -| `image` | Full-resolution tissue image, needed for `--segmentation_method cellpose` or `stardist` (optional) | -| `segmentation_file` | Cell segmentation for Visium HD, as GeoJSON or TIFF/NPY label mask, in full-resolution image pixels. (optional) | +| Column | Description | +| ------------------- | --------------------------------------------------------------------------------------------------------------- | +| `sample` | Unique sample identifier. | +| `spaceranger_dir` | Output directory generated by spaceranger. May be a `.tar.gz` file instead of a directory | +| `image` | Full-resolution tissue image, needed for `--segmentation_method cellpose` or `stardist` (optional) | +| `segmentation_file` | Cell segmentation for Visium HD, as GeoJSON or TIFF/NPY label mask, in full-resolution image pixels. (optional) | The Space Ranger output directory is typically called `outs` and contains both gene expression matrices as well as spatial information.