Threads documentation

Uploaded a spreadsheet with each task and their respective threads required.

docs/yaml_docs/threads_tasks_panpipes.csv

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+tasks ingest ,,,,,,,,,,,,,,,,,,
+Threads_high,Creating h5mu from filtered data files,Creating h5mu from bg data files, rna QC ,prot QC ,prot QC ,assess background,,,,,,,,,,,,
+threads_medium,load_mudatas,load_bg_mudatas,downsample_bg_mudatas,run_scrublet,,,,,,,,,,,,,,
+threads_low,run_repertoire_qc,run_atac_qc,plot_qc,10X metrics plotting,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+tasks preprocessed ,,,,,,,,,,,,,,,,,,
+Threads_high,rna_preprocess,prot_preprocess,atac_preprocess,,,,,,,,,,,,,,,
+threads_low,filter_mudata,postfilterplot,downsample,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+tasks integration  ,,,,,,,,,,,,,,,,,,
+Threads_high,run_no_batch_correct_rna,run_bbknn_rna,run_harmony_rna,run_combat_rna,run_scanorama_rna,run_scvi_rna,run_no_batch_correct_prot,run_harmony_prot,run_bbknn_prot,run_combat_prot,run_no_batch_correct_atac,run_harmony_atac,run_bbknn_atac,run_totalvi,run_multivi,run_mofa,run_wnn,merge_integration
+threads_medium,Evaluation,plot_umaps,run_scib_metrics,,,,,,,,,,,,,,,
+threads_low,run_lisi,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+tasks clustering ,,,,,,,,,,,,,,,,,,
+Threads_high,run_neighbors,run_umap,find_markers,,,,,,,,,,,,,,,
+threads_medium,run_clustering,collate_mdata,plot_cluster_umaps,plot_markers,,,,,,,,,,,,,,
+threads_low,clustering,clustering,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+tasks vis ,,,,,,,,,,,,,,,,,,
+Threads_high,plot_custom_markers_per_group,plot_custom_markers_umap,plot_categorical_umaps,write_obs,plot_scatters,,,,,,,,,,,,,
+threads_low,plot_metrics,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+tasks refmap ,,,,,,,,,,,,,,,,,,
+Threads_high,run_refmap_scvi,run_scib_refmap,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+tasks preprocessed spatial ,,,,,,,,,,,,,,,,,,
+Threads_high,spatial_preprocess,,,,,,,,,,,,,,,,,
+threads_low,filter_mudata,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,
+tasks  spatial ,,,,,,,,,,,,,,,,,,
+threads_medium,load_mudata,,,,,,,,,,,,,,,,,
+threads_low,plotQC_spatial,,,,,,,,,,,,,,,,,