From c5c2f0a3dcc8d68871406be46e08dcb9b8bf0c0f Mon Sep 17 00:00:00 2001 From: Sean Donahue Date: Thu, 28 Sep 2023 20:34:12 -0400 Subject: [PATCH] Marking data products in pipeline manifest --- pipeline-manifest.json | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/pipeline-manifest.json b/pipeline-manifest.json index 3b753e1..19dae57 100644 --- a/pipeline-manifest.json +++ b/pipeline-manifest.json @@ -2,7 +2,8 @@ { "pattern": "sprm_outputs/(?P.+)\\.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.+)\\.ome\\.tiff-normalized_cell_outlines.csv", @@ -12,7 +13,8 @@ { "pattern": "sprm_outputs/(?P.+)\\.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.+)\\.ome\\.tiff_AdjacencyMatrix_avg.mtx", @@ -22,7 +24,8 @@ { "pattern": "sprm_outputs/(?P.+)\\.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.+)\\.ome\\.tiff-cell_1_texture.csv", @@ -403,7 +406,8 @@ "pattern": "sprm_outputs/(?P.+)\\.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.+)\\.ome\\.tiff-superpixel.ome.tiff", @@ -459,6 +463,13 @@ "pattern": "sprm_outputs/(?P.+)\\.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 + } + ]