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Merge pull request #288 from DendrouLab/threads_doc_g
Threads documentation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,271 @@ | ||
| # Threads for individual workflow tasks | ||
|
|
||
| <table> | ||
| <tr> | ||
| <th colspan="3">Task ingest</th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th>threads_medium</th> | ||
| <th>threads_low</th> | ||
| </tr> | ||
| <tr> | ||
| <td>Creating h5mu from filtered data files</td> | ||
| <td>load_mudatas</td> | ||
| <td>run_repertoire_qc</td> | ||
| </tr> | ||
| <tr> | ||
| <td>Creating h5mu from bg data files</td> | ||
| <td>load_bg_mudatas</td> | ||
| <td>run_atac_qc</td> | ||
| </tr> | ||
| <tr> | ||
| <td>rna QC</td> | ||
| <td>downsample_bg_mudatas</td> | ||
| <td>plot_qc</td> | ||
| </tr> | ||
| <tr> | ||
| <td>prot QC</td> | ||
| <td>run_scrublet</td> | ||
| <td>10X metrics plotting</td> | ||
| </tr> | ||
| <tr> | ||
| <td>prot QC</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <th colspan="3">Task preprocess</th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th>threads_medium</th> | ||
| <th>threads_low</th> | ||
| <th></th> | ||
| <th></th> | ||
| </tr> | ||
| <tr> | ||
| <td>assess background</td> | ||
| <td></td> | ||
| <td>filter_mudata</td> | ||
| </tr> | ||
| <tr> | ||
| <td>rna_preprocess</td> | ||
| <td></td> | ||
| <td>downsample</td> | ||
| </tr> | ||
| <tr> | ||
| <td>prot_preprocess</td> | ||
| <td></td> | ||
| <td>postfilterplot</td> | ||
| </tr> | ||
| <tr> | ||
| <td>atac_preprocess</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <th colspan="3">Task integration</th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th>threads_medium</th> | ||
| <th>threads_low</th> | ||
| </tr> | ||
| <tr> | ||
| <td>run_no_batch_correct_rna</td> | ||
| <td>Evaluation</td> | ||
| <td>run_lisi</td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_bbknn_rna</td> | ||
| <td>plot_umaps</td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_harmony_rna</td> | ||
| <td>run_scib_metrics</td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_combat_rna</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_scanorama_rna</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_scvi_rna</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_no_batch_correct_prot</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_harmony_prot</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_bbknn_prot</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_combat_prot</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_no_batch_correct_atac</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_harmony_atac</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_bbknn_atac</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_totalvi</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_multivi</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_mofa</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_wnn</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>merge_integration</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <th colspan="3">Task clustering</th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th>threads_medium</th> | ||
| <th>threads_low</th> | ||
| </tr> | ||
| <tr> | ||
| <td>run_neighbors</td> | ||
| <td>run_clustering</td> | ||
| <td>plot_clustree</td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_umap</td> | ||
| <td>collate_mdata</td> | ||
| <td>aggregate_clusters</td> | ||
| </tr> | ||
| <tr> | ||
| <td>find_markers</td> | ||
| <td>plot_cluster_umaps</td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td></td> | ||
| <td>plot_markers</td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <th colspan="3">Task vis</th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th></th> | ||
| <th>threads_low</th> | ||
| </tr> | ||
| <tr> | ||
| <td>plot_custom_markers_per_group</td> | ||
| <td></td> | ||
| <td>plot_metrics</td> | ||
| </tr> | ||
| <tr> | ||
| <td>plot_custom_markers_umap</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>plot_categorical_umaps</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>write_obs</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>plot_scatters</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <th colspan = "3"> Task refmap </th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th><th> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_refmap_scvi</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <td>run_scib_refmap</td> | ||
| <td></td> | ||
| <td></td> | ||
| </tr> | ||
| <tr> | ||
| <th colspan="3">Task preprocess spatial</th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th></th> | ||
| <th>threads_low</th> | ||
| </tr> | ||
| <tr> | ||
| <td>spatial_preprocess</td> | ||
| <td></td> | ||
| <td>filter_mudata</td> | ||
| </tr> | ||
| <tr> | ||
| <th colspan="3">Task Spatial</th> | ||
| </tr> | ||
| <tr> | ||
| <th>threads_high</th> | ||
| <th></th> | ||
| <th>threads_low</th> | ||
| </tr> | ||
| <tr> | ||
| <td>load_mudata</td> | ||
| <td></td> | ||
| <td>plotQC_spatial</td> | ||
| </tr> | ||
| </table> |