@include "rna/_sc_rna_analyzer_stages.mro"

call SUMMARIZE_ANALYSIS(
    matrix_h5                     = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-ua092a47512/files/preprocessed_matrix_h5.h5",
    pca_h5                        = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-ua092a4751a/files/pca_h5.h5",
    clustering_h5                 = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-ua092a4752c/files/clustering_h5.h5",
    diffexp_h5                    = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-ua092a4752c/files/diffexp_h5.h5",
    tsne_h5                       = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-ua092a47524/files/tsne_h5.h5",
    umap_h5                       = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-ua092a47524/files/umap_h5.h5",
    pca_csv                       = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-ua092a4751a/files/pca_csv",
    clustering_csv                = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-ua092a4752c/files/clustering_csv",
    diffexp_csv                   = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-ua092a4752c/files/diffexp_csv",
    tsne_csv                      = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-ua092a47524/files/tsne_csv",
    umap_csv                      = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-ua092a47524/files/umap_csv",
    multi_genome_summary          = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-ua092a4751a/files/multi_genome_summary.json",
    multi_genome_csv              = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-ua092a4751a/files/multi_genome_csv",
    multi_genome_json             = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-ua092a4751a/files/multi_genome_json",
    is_multi_genome               = false,
    chemistry_batch_correction    = false,
    batch_score_before_correction = null,
    batch_score_after_correction  = null,
)
