@include "rna/_sc_rna_analyzer_stages.mro"

call SUMMARIZE_ANALYSIS(
    matrix_h5                     = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-uac0168ab19/files/preprocessed_matrix_h5.h5",
    pca_h5                        = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/CHOOSE_DIMENSION_REDUCTION_OUTPUT/fork0/chnk0-uac0168abc3/files/pca_h5.h5",
    clustering_h5                 = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-uac0168abfc/files/clustering_h5.h5",
    diffexp_h5                    = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-uac0168abfc/files/diffexp_h5.h5",
    tsne_h5                       = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-uac0168abc4/files/tsne_h5.h5",
    umap_h5                       = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-uac0168abc4/files/umap_h5.h5",
    pca_csv                       = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/CHOOSE_DIMENSION_REDUCTION_OUTPUT/fork0/chnk0-uac0168abc3/files/pca_csv",
    clustering_csv                = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-uac0168abfc/files/clustering_csv",
    diffexp_csv                   = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-uac0168abfc/files/diffexp_csv",
    tsne_csv                      = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-uac0168abc4/files/tsne_csv",
    umap_csv                      = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-uac0168abc4/files/umap_csv",
    multi_genome_summary          = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-uac0168ab34/files/multi_genome_summary.json",
    multi_genome_csv              = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-uac0168ab34/files/multi_genome_csv",
    multi_genome_json             = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-uac0168ab34/files/multi_genome_json",
    is_multi_genome               = false,
    chemistry_batch_correction    = false,
    batch_score_before_correction = null,
    batch_score_after_correction  = null,
    skip                          = false,
)
