Workflow: spatial transcriptomics pipeline including analysis with scanpy and squidpy
Fetched 2026-08-24 14:29:49 GMT
Verified with cwltool version 3.1.20230201224320
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source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| assay | String | scRNA-seq assay | |
| data_dir | Directory | Directory containing FASTQ files |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| convert_formats |
steps/convert-formats.cwl
(CommandLineTool)
|
Convert Alevin sparse output to anndata.AnnData object, save as h5ad | |
| scanpy_analysis |
steps/scanpy-analysis.cwl
(CommandLineTool)
|
Dimensionality reduction and clustering | |
| squidpy_analysis |
steps/squidpy-analysis.cwl
(CommandLineTool)
|
Dimensionality reduction and clustering | |
| compute_qc_results |
steps/compute-qc-metrics.cwl
(CommandLineTool)
|
Compute QC metrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| umap_plot | File | UMAP dimensionality reduction plot | |
| ripley_plot | File (Optional) | ||
| spatial_plot | File (Optional) | Slide-seq bead plot, colored by Leiden cluster | |
| sdata_zarr_zip | File | SpatialData object serialized in zarr format | |
| dispersion_plot | File | Gene expression dispersion plot | |
| count_matrix_h5ad | File | Count matrix converted to h5ad | |
| scanpy_qc_results | File | Quality control metrics from Scanpy | |
| umap_density_plot | File | UMAP dimensionality reduction plot, colored by cell density | |
| co_occurrence_plot | File (Optional) | ||
| filtered_data_h5ad | File | Full data set of filtered results |
Full data set of filtered results: expression matrix, coordinates in dimensionality-reduced space (PCA and UMAP), cluster assignments via the Leiden algorithm, and marker genes for one cluster vs. rest |
| squidpy_spatial_plot | File (Optional) | ||
| centrality_scores_plot | File (Optional) | ||
| squidpy_annotated_h5ad | File (Optional) | ||
| interaction_matrix_plot | File (Optional) | ||
| marker_gene_plot_logreg | File | Cluster marker genes, logreg method | |
| marker_gene_plot_t_test | File | Cluster marker genes, t-test | |
| neighborhood_enrichment_plot | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/3a861e0dda09983a89e7ab48ab57c16d07e75dbe/pipeline.cwl
