From d14d2b0b3fc3d0f49b9e224f112bc8048323b1ff Mon Sep 17 00:00:00 2001 From: bistline Date: Tue, 17 Sep 2024 14:21:35 -0400 Subject: [PATCH] Fixing demo command line for AnnData DE --- ingest/ingest_pipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ingest/ingest_pipeline.py b/ingest/ingest_pipeline.py index 68fc348b..6300fd65 100644 --- a/ingest/ingest_pipeline.py +++ b/ingest/ingest_pipeline.py @@ -67,7 +67,7 @@ python ingest_pipeline.py --study-id addedfeed000000000000000 --study-file-id dec0dedfeed1111111111111 differential_expression --annotation-name cell_type__ontology_label --annotation-type group --annotation-scope study --matrix-file-path ../tests/data/differential_expression/sparse/sparsemini_matrix.mtx --gene-file ../tests/data/differential_expression/sparse/sparsemini_features.tsv --barcode-file ../tests/data/differential_expression/sparse/sparsemini_barcodes.tsv --matrix-file-type mtx --annotation-file ../tests/data/differential_expression/sparse/sparsemini_metadata.txt --cluster-file ../tests/data/differential_expression/sparse/sparsemini_cluster.txt --cluster-name de_sparse_integration --study-accession SCPsparsemini --differential-expression # Differential expression analysis (h5ad matrix) -python ingest_pipeline.py --study-id addedfeed000000000000000 --study-file-id dec0dedfeed1111111111111 differential_expression --annotation-name cell_type__ontology_label --annotation-type group --annotation-scope study --matrix-file-path ../tests/data/differential_expression/de_dense_matrix.tsv --matrix-file-type h5ad --annotation-file ../tests/data/differential_expression/de_dense_metadata.tsv --cluster-file ../tests/data/differential_expression/de_dense_cluster.tsv --cluster-name de_integration --study-accession SCPdev --differential-expression +python ingest_pipeline.py --study-id addedfeed000000000000000 --study-file-id dec0dedfeed1111111111111 differential_expression --annotation-name louvain --annotation-type group --annotation-scope study --matrix-file-path ../tests/data/anndata/trimmed_compliant_pbmc3K.h5ad --matrix-file-type h5ad --annotation-file ../tests/data/anndata/h5ad_frag.metadata.tsv --cluster-file ../tests/data/anndata/h5ad_frag.cluster.X_umap.tsv --cluster-name umap --study-accession SCPdev --differential-expression """ import json