@include "rna/_sc_rna_analyzer_stages.mro"

call SUMMARIZE_ANALYSIS(
    matrix_h5                     = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-ue5873db267/files/preprocessed_matrix_h5.h5",
    pca_h5                        = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/CHOOSE_DIMENSION_REDUCTION_OUTPUT/fork0/chnk0-ue5873db279/files/pca_h5.h5",
    clustering_h5                 = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-ue5873db28b/files/clustering_h5.h5",
    diffexp_h5                    = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-ue5873db28c/files/diffexp_h5.h5",
    tsne_h5                       = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/RUN_TSNE/fork0/join-ue5873db279/files/tsne_h5.h5",
    umap_h5                       = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/RUN_UMAP/fork0/join-ue5873db279/files/umap_h5.h5",
    pca_csv                       = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/CHOOSE_DIMENSION_REDUCTION_OUTPUT/fork0/chnk0-ue5873db279/files/pca_csv",
    clustering_csv                = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-ue5873db28b/files/clustering_csv",
    diffexp_csv                   = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-ue5873db28c/files/diffexp_csv",
    tsne_csv                      = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/RUN_TSNE/fork0/join-ue5873db279/files/tsne_csv",
    umap_csv                      = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/RUN_UMAP/fork0/join-ue5873db279/files/umap_csv",
    multi_genome_summary          = null,
    multi_genome_csv              = null,
    multi_genome_json             = null,
    is_multi_genome               = false,
    chemistry_batch_correction    = false,
    batch_score_before_correction = null,
    batch_score_after_correction  = null,
    skip                          = false,
)
