From 73101661034b5a80aab64ec403d525f980817da9 Mon Sep 17 00:00:00 2001 From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com> Date: Thu, 20 Jun 2024 14:50:13 +0100 Subject: [PATCH] Threads documentation Uploaded a spreadsheet with each task and their respective threads required. --- docs/yaml_docs/threads_tasks_panpipes.csv | 49 +++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 docs/yaml_docs/threads_tasks_panpipes.csv diff --git a/docs/yaml_docs/threads_tasks_panpipes.csv b/docs/yaml_docs/threads_tasks_panpipes.csv new file mode 100644 index 00000000..b5da1db6 --- /dev/null +++ b/docs/yaml_docs/threads_tasks_panpipes.csv @@ -0,0 +1,49 @@ +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,,,,,,,,,,,,,,,,, \ No newline at end of file