@include "_sc_rna_analyzer_stages.mro"

call SUMMARIZE_ANALYSIS(
    matrix_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u85e8948c0d/files/preprocessed_matrix_h5.h5",
    pca_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/CHOOSE_DIMENSION_REDUCTION_OUTPUT/fork0/chnk0-u85e8949a63/files/pca_h5.h5",
    clustering_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u85e8949bc0/files/clustering_h5.h5",
    diffexp_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u85e8949bc5/files/diffexp_h5.h5",
    tsne_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-u85e8949a68/files/tsne_h5.h5",
    umap_h5 = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u85e8949a68/files/umap_h5.h5",
    pca_csv = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/CHOOSE_DIMENSION_REDUCTION_OUTPUT/fork0/chnk0-u85e8949a63/files/pca_csv",
    clustering_csv = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u85e8949bc0/files/clustering_csv",
    diffexp_csv = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u85e8949bc5/files/diffexp_csv",
    tsne_csv = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-u85e8949a68/files/tsne_csv",
    umap_csv = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u85e8949a68/files/umap_csv",
    multi_genome_summary = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u85e8949a2a/files/multi_genome_summary.json",
    multi_genome_csv = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u85e8949a2a/files/multi_genome_csv",
    multi_genome_json = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u85e8949a2a/files/multi_genome_json",
    is_multi_genome = false,
    chemistry_batch_correction = false,
    batch_score_before_correction = null,
    batch_score_after_correction = null,
    skip = false,
)