From 878277e2d3c714caada4464f6951dd5dff41d63b Mon Sep 17 00:00:00 2001 From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com> Date: Tue, 15 Oct 2024 17:45:13 +0100 Subject: [PATCH] Update threads_tasks_panpipes.csv --- docs/yaml_docs/threads_tasks_panpipes.csv | 76 ++++++++--------------- 1 file changed, 27 insertions(+), 49 deletions(-) diff --git a/docs/yaml_docs/threads_tasks_panpipes.csv b/docs/yaml_docs/threads_tasks_panpipes.csv index b5da1db6..484e88af 100644 --- a/docs/yaml_docs/threads_tasks_panpipes.csv +++ b/docs/yaml_docs/threads_tasks_panpipes.csv @@ -1,49 +1,27 @@ -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 +| **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 | | | | | | | | | | | | | | | | | |