pipeline-manifest.json

[
	{
		"pattern": "secondary_analysis\\.h5ad",
		"description": "Normalized gene expression with additional metadata, in HDF5 format, readable with the 'anndata' Python package",
		"edam_ontology_term": "EDAM_1.24.format_3590"
	},
	{
		"pattern": "scvelo_annotated\\.h5ad",
		"description": "RNA velocity results, in HDF5 format, readable with the 'anndata' Python package",
		"edam_ontology_term": "EDAM_1.24.format_3590"
	},
	{
		"pattern": "expr\\.h5ad",
		"description": "Raw gene expression, in HDF5 format, readable with the 'anndata' Python package, intronic counts collapsed to genes",
		"edam_ontology_term": "EDAM_1.24.format_3590"
	},
	{
		"pattern": "raw_expr\\.h5ad",
		"description": "Raw gene expression, in HDF5 format, readable with the 'anndata' Python package, with intronic counts",
		"edam_ontology_term": "EDAM_1.24.format_3590"
	},
	{
		"pattern": "qc_results\\.hdf5",
		"description": "Quality control results from Scanpy, per-cell and per-gene, in HDF5 format",
		"edam_ontology_term": "EDAM_1.24.format_3590",
		"is_qa_qc": true
	},
	{
		"pattern": "qc_results\\.json",
		"description": "Quality control report in JSON format",
		"edam_ontology_term": "EDAM_1.24.format_3464",
		"is_qa_qc": true
	},
	{
		"pattern": "dispersion_plot\\.pdf",
		"description": "Disperson plot of gene expression",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "umap_by_leiden_cluster\\.pdf",
		"description": "UMAP plot of cells, colored by Leiden cluster ID",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "umap_embedding_density\\.pdf",
		"description": "UMAP plot of cells, colored by embedding density",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "umap_embedding_density\\.pdf",
		"description": "UMAP plot of cells, colored by embedding density",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "spatial_pos_by_leiden_cluster\\.pdf",
		"description": "Spatial plot of cells, colored by Leiden cluster ID",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "scvelo_embedding_grid\\.pdf",
		"description": "scVelo RNA velocity grid plot",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "scvelo_embedding_stream\\.pdf",
		"description": "scVelo RNA velocity stream plot",
		"edam_ontology_term": "EDAM_1.24.format_3508"
	},
	{
		"pattern": "fastqc_output/.*\\.html",
		"description": "FastQC report of input FASTQ file",
		"edam_ontology_term": "EDAM_1.24.format_2331",
		"is_qa_qc": true
	}
]