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Marking data products in pipeline manifest #19

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Marking data products in pipeline manifest #19

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21 changes: 16 additions & 5 deletions pipeline-manifest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,8 @@
{
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyGraph.pdf",
"description": "Spatial adjacency graph of cells and their connected neighbors.",
"edam_ontology_term": "EDAM_1.24.format_3508"
"edam_ontology_term": "EDAM_1.24.format_3508",
"is_data_product": true
},
{
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-normalized_cell_outlines.csv",
Expand All @@ -12,7 +13,8 @@
{
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyMatrix.mtx",
"description": "Sparse matrix output of cell adjacency matrix for minimal distance.",
"edam_ontology_term": "EDAM_1.24.format_3916"
"edam_ontology_term": "EDAM_1.24.format_3916",
"is_data_product": true
},
{
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyMatrix_avg.mtx",
Expand All @@ -22,7 +24,8 @@
{
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_AdjacencyMatrixRowColLabels.txt",
"description": "text file of row and column label for adjacency matrix.",
"edam_ontology_term": "EDAM_1.24.data_3671"
"edam_ontology_term": "EDAM_1.24.data_3671",
"is_data_product": true
},
{
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-cell_1_texture.csv",
Expand Down Expand Up @@ -403,7 +406,8 @@
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-SPRM_Image_Quality_Measures.json",
"description": "Image Quality Measures.",
"edam_ontology_term": "EDAM_1.24.format_3464",
"is_qa_qc": true
"is_qa_qc": true,
"is_data_product": true
},
{
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff-superpixel.ome.tiff",
Expand Down Expand Up @@ -459,6 +463,13 @@
"pattern": "sprm_outputs/(?P<region>.+)\\.ome\\.tiff_nmf_components.pdf",
"description": "dimensionality reduction by NMF (Non-Negative Matrix Factorization) on image and heat map visualization of their components",
"edam_ontology_term": "EDAM_1.24.format_3752"
}
},
{
"pattern": "out.hdf5",
"description": "hdf5 file containing DataFrames for each of SPRM's CSV outputs, including expression values, cluster assignments",
"edam_ontology_term": "EDAM_1.24.format_3590",
"is_data_product": true
}

]