diff --git a/docs/yaml_docs/index.rst b/docs/yaml_docs/index.rst index 4109eea6..e517d1be 100644 --- a/docs/yaml_docs/index.rst +++ b/docs/yaml_docs/index.rst @@ -14,5 +14,6 @@ Workflows configuration files spatial_deconvolution pipeline_visualization_yml pipeline_refmap_yml + threads_tasks_panpipes diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md index 8389b328..e7f88a87 100644 --- a/docs/yaml_docs/pipeline_clustering_yml.md +++ b/docs/yaml_docs/pipeline_clustering_yml.md @@ -31,7 +31,7 @@ You can download the different clustering pipeline.yml files here: ## Compute resources options - resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs, Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 2
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md index 55e7c457..9cda82d3 100644 --- a/docs/yaml_docs/pipeline_ingestion_yml.md +++ b/docs/yaml_docs/pipeline_ingestion_yml.md @@ -31,7 +31,7 @@ You can download the different ingestion `pipeline.yml` files here: ## Compute resources options resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 1
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md index bb31f119..97241f37 100644 --- a/docs/yaml_docs/pipeline_integration_yml.md +++ b/docs/yaml_docs/pipeline_integration_yml.md @@ -23,7 +23,7 @@ For more information on functionalities implemented in `panpipes` to read the co ## Compute resources options resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following parameters: - threads_high `Integer`, Default: 1
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md index 634fbc34..884c3f7f 100644 --- a/docs/yaml_docs/pipeline_preprocess_yml.md +++ b/docs/yaml_docs/pipeline_preprocess_yml.md @@ -27,7 +27,7 @@ You can download the different preprocess `pipeline.yml` files here: ## Compute resources options resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs.Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 2
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/pipeline_refmap_yml.md b/docs/yaml_docs/pipeline_refmap_yml.md index d3222c5e..803747a5 100644 --- a/docs/yaml_docs/pipeline_refmap_yml.md +++ b/docs/yaml_docs/pipeline_refmap_yml.md @@ -27,7 +27,7 @@ You can download the different refmap `pipeline.yml` files here: ## Compute resources options resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 1
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/pipeline_visualization_yml.md b/docs/yaml_docs/pipeline_visualization_yml.md index f5c26330..07c9251d 100644 --- a/docs/yaml_docs/pipeline_visualization_yml.md +++ b/docs/yaml_docs/pipeline_visualization_yml.md @@ -24,7 +24,7 @@ You can download the different ingestion `pipeline.yml` files here: ## Compute resources options resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 1
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/spatial_deconvolution.md b/docs/yaml_docs/spatial_deconvolution.md index 29a4e93a..6aa04c46 100644 --- a/docs/yaml_docs/spatial_deconvolution.md +++ b/docs/yaml_docs/spatial_deconvolution.md @@ -26,7 +26,7 @@ For more information on functionalities implemented in `panpipes` to read the co ## 0. Compute Resource Options resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 1
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/spatial_preprocess.md b/docs/yaml_docs/spatial_preprocess.md index 28270c99..9100546f 100644 --- a/docs/yaml_docs/spatial_preprocess.md +++ b/docs/yaml_docs/spatial_preprocess.md @@ -28,7 +28,7 @@ You can download the different preprocess pipeline.yml files here: ## 0. Compute Resource Options resources
-Computing resources to use, specifically the number of threads used for parallel jobs. +Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 1
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/spatial_qc.md b/docs/yaml_docs/spatial_qc.md index 5a742ab0..5ccbac7a 100644 --- a/docs/yaml_docs/spatial_qc.md +++ b/docs/yaml_docs/spatial_qc.md @@ -29,6 +29,7 @@ For more information on functionalities implemented in `panpipes` to read the co resources
Computing resources to use, specifically the number of threads used for parallel jobs. +Check [threads_tasks_panpipes](./threads_tasks_panpipes.md) for more information on which threads each specific task requires. Specified by the following three parameters: - threads_high `Integer`, Default: 1
Number of threads used for high intensity computing tasks. diff --git a/docs/yaml_docs/threads_tasks_panpipes.md b/docs/yaml_docs/threads_tasks_panpipes.md new file mode 100644 index 00000000..72c90956 --- /dev/null +++ b/docs/yaml_docs/threads_tasks_panpipes.md @@ -0,0 +1,271 @@ +# Threads for individual workflow tasks + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Task ingest
threads_highthreads_mediumthreads_low
Creating h5mu from filtered data filesload_mudatasrun_repertoire_qc
Creating h5mu from bg data filesload_bg_mudatasrun_atac_qc
rna QCdownsample_bg_mudatasplot_qc
prot QCrun_scrublet10X metrics plotting
prot QC
Task preprocess
threads_highthreads_mediumthreads_low
assess backgroundfilter_mudata
rna_preprocessdownsample
prot_preprocesspostfilterplot
atac_preprocess
Task integration
threads_highthreads_mediumthreads_low
run_no_batch_correct_rnaEvaluationrun_lisi
run_bbknn_rnaplot_umaps
run_harmony_rnarun_scib_metrics
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
Task clustering
threads_highthreads_mediumthreads_low
run_neighborsrun_clusteringplot_clustree
run_umapcollate_mdataaggregate_clusters
find_markersplot_cluster_umaps
plot_markers
Task vis
threads_highthreads_low
plot_custom_markers_per_groupplot_metrics
plot_custom_markers_umap
plot_categorical_umaps
write_obs
plot_scatters
Task refmap
threads_high +
run_refmap_scvi
run_scib_refmap
Task preprocess spatial
threads_highthreads_low
spatial_preprocessfilter_mudata
Task Spatial
threads_highthreads_low
load_mudataplotQC_spatial