From 9313fd72f249f5b55e54f1ca2454694dbcefcdb5 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:18:08 +0100
Subject: [PATCH 01/51] Threads tasks

Spreadsheet with each threads required for all tasks.
---
 docs/yaml_docs/threads_tasks_panpipes.xlsx | Bin 0 -> 10970 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 docs/yaml_docs/threads_tasks_panpipes.xlsx

diff --git a/docs/yaml_docs/threads_tasks_panpipes.xlsx b/docs/yaml_docs/threads_tasks_panpipes.xlsx
new file mode 100644
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From 1c60c5e815878a4cd2bc9a15e55700b546969b94 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:19:08 +0100
Subject: [PATCH 02/51] Update index.rst

---
 docs/yaml_docs/index.rst | 1 +
 1 file changed, 1 insertion(+)

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
 
 

From b939250097fa5fb1478daa913866939871ba7245 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:22:11 +0100
Subject: [PATCH 03/51] Update pipeline_clustering_yml.md

---
 docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 8389b328..6f60f77d 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
 
 - <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires. 
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From 13836f1bcafaf0a62997eee4c7df8c6e217729ba Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:27:15 +0100
Subject: [PATCH 04/51] Update pipeline_ingestion_yml.md

---
 docs/yaml_docs/pipeline_ingestion_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
index 55e7c457..0479aa18 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
 
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 6886b2abb3e711f77c7999b9d9a2a17d2e51a5a3 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:27:35 +0100
Subject: [PATCH 05/51] Update pipeline_integration_yml.md

---
 docs/yaml_docs/pipeline_integration_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md
index ab81905c..da27ba3a 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
 
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
    Number of threads used for high intensity computing tasks. 

From e46b1666a20b15f6c7afcb5e43c8e326695edf86 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:27:52 +0100
Subject: [PATCH 06/51] Update pipeline_preprocess_yml.md

---
 docs/yaml_docs/pipeline_preprocess_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md
index 634fbc34..158a8df8 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
 
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From 65e38cf30d9acb3b0307a013e510f5767e504b06 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:28:19 +0100
Subject: [PATCH 07/51] Update pipeline_refmap_yml.md

---
 docs/yaml_docs/pipeline_refmap_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_refmap_yml.md b/docs/yaml_docs/pipeline_refmap_yml.md
index d3222c5e..918154e2 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
 
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
 Number of threads used for high intensity computing tasks. 

From 765fef95a904363812a195f5262f9efd41d57adc Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:28:49 +0100
Subject: [PATCH 08/51] Update pipeline_visualization_yml.md

---
 docs/yaml_docs/pipeline_visualization_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_visualization_yml.md b/docs/yaml_docs/pipeline_visualization_yml.md
index f5c26330..ca3ce38f 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
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From d68f5ee198adaa1a2e63ebe4e82e3f161248100d Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:29:47 +0100
Subject: [PATCH 09/51] Update spatial_deconvolution.md

---
 docs/yaml_docs/spatial_deconvolution.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_deconvolution.md b/docs/yaml_docs/spatial_deconvolution.md
index 29a4e93a..9b37f85f 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
 
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From c005711da402895c287f138fa6121f37eec011a2 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:30:16 +0100
Subject: [PATCH 10/51] Update spatial_preprocess.md

---
 docs/yaml_docs/spatial_preprocess.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_preprocess.md b/docs/yaml_docs/spatial_preprocess.md
index 28270c99..df150c72 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
 
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 9c6b886a608dc101c0c00a0a7263a8ce34bb230c Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:30:38 +0100
Subject: [PATCH 11/51] Update spatial_qc.md

---
 docs/yaml_docs/spatial_qc.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_qc.md b/docs/yaml_docs/spatial_qc.md
index 5a742ab0..b28ffb7a 100644
--- a/docs/yaml_docs/spatial_qc.md
+++ b/docs/yaml_docs/spatial_qc.md
@@ -28,7 +28,7 @@ For more information on functionalities implemented in `panpipes` to read the co
 
 
 <span class="parameter">resources</span><br>
-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.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From c4fc55cc4b8a254677176c2aef5996dd657bcd06 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:45:01 +0100
Subject: [PATCH 12/51] Delete docs/yaml_docs/threads_tasks_panpipes.xlsx

---
 docs/yaml_docs/threads_tasks_panpipes.xlsx | Bin 10970 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 docs/yaml_docs/threads_tasks_panpipes.xlsx

diff --git a/docs/yaml_docs/threads_tasks_panpipes.xlsx b/docs/yaml_docs/threads_tasks_panpipes.xlsx
deleted file mode 100644
index 90b4d756368237627863e7c106ec3cd9cd0b9f6f..0000000000000000000000000000000000000000
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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 13/51] 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

From 9cb92e9a946759a8fa9ba26d05be645548622153 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:52:38 +0100
Subject: [PATCH 14/51] Update pipeline_clustering_yml.md

---
 docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 6f60f77d..db3b03ad 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
 
 - <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires. 
+Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires. 
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From b76b14981a2a2834dbdd84b7ef88bd6461528157 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:52:58 +0100
Subject: [PATCH 15/51] Update pipeline_ingestion_yml.md

---
 docs/yaml_docs/pipeline_ingestion_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
index 0479aa18..9ff9744c 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs,  check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 582db349470e86e9b4182a505167eab9d52bfb49 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:53:19 +0100
Subject: [PATCH 16/51] Update pipeline_integration_yml.md

---
 docs/yaml_docs/pipeline_integration_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md
index da27ba3a..b8548e26 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
    Number of threads used for high intensity computing tasks. 

From 866d12a81d46ba644f8f4a753555da7b5fa107fa Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:53:44 +0100
Subject: [PATCH 17/51] Update pipeline_preprocess_yml.md

---
 docs/yaml_docs/pipeline_preprocess_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md
index 158a8df8..16279e51 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From 6ca45304f9c9b1732a9ea893619101aeae9fe300 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:54:05 +0100
Subject: [PATCH 18/51] Update pipeline_refmap_yml.md

---
 docs/yaml_docs/pipeline_refmap_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_refmap_yml.md b/docs/yaml_docs/pipeline_refmap_yml.md
index 918154e2..d292c1b0 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
 Number of threads used for high intensity computing tasks. 

From 2c991f429303cc66405577a11657ff6ff1653e1c Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:54:52 +0100
Subject: [PATCH 19/51] Update pipeline_visualization_yml.md

---
 docs/yaml_docs/pipeline_visualization_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_visualization_yml.md b/docs/yaml_docs/pipeline_visualization_yml.md
index ca3ce38f..d6a2a08d 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
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 95ce2efbe6315d25a174523daf4511edb4fd0e82 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:55:16 +0100
Subject: [PATCH 20/51] Update spatial_deconvolution.md

---
 docs/yaml_docs/spatial_deconvolution.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_deconvolution.md b/docs/yaml_docs/spatial_deconvolution.md
index 9b37f85f..afbd4c87 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 3971ab208648fd95d4f1287f986e74262b432b03 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:55:52 +0100
Subject: [PATCH 21/51] Update spatial_preprocess.md

---
 docs/yaml_docs/spatial_preprocess.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_preprocess.md b/docs/yaml_docs/spatial_preprocess.md
index df150c72..8575d199 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 28ca7eae86def55286e87ba7fbf1afb43307594f Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:56:27 +0100
Subject: [PATCH 22/51] Update spatial_qc.md

---
 docs/yaml_docs/spatial_qc.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_qc.md b/docs/yaml_docs/spatial_qc.md
index b28ffb7a..3081a025 100644
--- a/docs/yaml_docs/spatial_qc.md
+++ b/docs/yaml_docs/spatial_qc.md
@@ -28,7 +28,7 @@ For more information on functionalities implemented in `panpipes` to read the co
 
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.xlsx) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From bfac191758d58476246b07f999780e6424336d46 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:56:54 +0100
Subject: [PATCH 23/51] Update pipeline_clustering_yml.md

---
 docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index db3b03ad..f2b73c37 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
 
 - <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires. 
+Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires. 
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From e7a2c40314c89c57c9ca3d42c389c63b6286bc64 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:57:10 +0100
Subject: [PATCH 24/51] Update pipeline_ingestion_yml.md

---
 docs/yaml_docs/pipeline_ingestion_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
index 9ff9744c..cd1dd293 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs,  check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs,  check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 9c9c83a46429a9dca1c3fc91f64117aa501d4ac6 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:57:30 +0100
Subject: [PATCH 25/51] Update pipeline_integration_yml.md

---
 docs/yaml_docs/pipeline_integration_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md
index b8548e26..50f63497 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
    Number of threads used for high intensity computing tasks. 

From 9f2e0402976de87ab6af2bd3c05d7e6a29239b2f Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:57:50 +0100
Subject: [PATCH 26/51] Update pipeline_preprocess_yml.md

---
 docs/yaml_docs/pipeline_preprocess_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md
index 16279e51..3ecf79cf 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From acf4835a05b68fe820349d76ef023f3638e1a18d Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:58:05 +0100
Subject: [PATCH 27/51] Update pipeline_refmap_yml.md

---
 docs/yaml_docs/pipeline_refmap_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_refmap_yml.md b/docs/yaml_docs/pipeline_refmap_yml.md
index d292c1b0..3a98d6f9 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
 Number of threads used for high intensity computing tasks. 

From 2e06eea99d33e22e0ad9604a4490d13c6ff6dc13 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:58:20 +0100
Subject: [PATCH 28/51] Update pipeline_visualization_yml.md

---
 docs/yaml_docs/pipeline_visualization_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_visualization_yml.md b/docs/yaml_docs/pipeline_visualization_yml.md
index d6a2a08d..278143b9 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
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 27945f548d854be24776e59f9477bebc9019b661 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:58:43 +0100
Subject: [PATCH 29/51] Update spatial_deconvolution.md

---
 docs/yaml_docs/spatial_deconvolution.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_deconvolution.md b/docs/yaml_docs/spatial_deconvolution.md
index afbd4c87..1e876ee2 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.xlsx](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

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 30/51] 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                         	|                                  	|                        	|                      	|                   	|                   	|                           	|                  	|                	|                 	|                           	|                  	|                	|             	|             	|          	|         	|                   	|

From e0b2a21563db08f01bd518488fc841a729561dc5 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 15 Oct 2024 18:30:58 +0100
Subject: [PATCH 31/51] Updated to an HTML table

Turned the csv into an HTML
---
 docs/yaml_docs/threads_tasks_panpipes.csv |  27 ---
 docs/yaml_docs/threads_tasks_panpipes.md  | 268 ++++++++++++++++++++++
 2 files changed, 268 insertions(+), 27 deletions(-)
 delete mode 100644 docs/yaml_docs/threads_tasks_panpipes.csv
 create mode 100644 docs/yaml_docs/threads_tasks_panpipes.md

diff --git a/docs/yaml_docs/threads_tasks_panpipes.csv b/docs/yaml_docs/threads_tasks_panpipes.csv
deleted file mode 100644
index 484e88af..00000000
--- a/docs/yaml_docs/threads_tasks_panpipes.csv
+++ /dev/null
@@ -1,27 +0,0 @@
-| **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                         	|                                  	|                        	|                      	|                   	|                   	|                           	|                  	|                	|                 	|                           	|                  	|                	|             	|             	|          	|         	|                   	|
diff --git a/docs/yaml_docs/threads_tasks_panpipes.md b/docs/yaml_docs/threads_tasks_panpipes.md
new file mode 100644
index 00000000..185faecb
--- /dev/null
+++ b/docs/yaml_docs/threads_tasks_panpipes.md
@@ -0,0 +1,268 @@
+<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 preprocessed</th>
+  </tr>
+  <tr>
+    <th>threads_high</th>
+    <th></th>
+    <th></th>
+  </tr>
+  <tr>
+    <td>assess background</td>
+    <td></td>
+    <td>threads_low</td>
+  </tr>
+  <tr>
+    <td>rna_preprocess</td>
+    <td></td>
+    <td>filter_mudata</td>
+  </tr>
+  <tr>
+    <td>prot_preprocess</td>
+    <td></td>
+    <td>postfilterplot</td>
+  </tr>
+  <tr>
+    <td>atac_preprocess</td>
+    <td></td>
+    <td>downsample</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>clustering</td>
+  </tr>
+  <tr>
+    <td>run_umap</td>
+    <td>collate_mdata</td>
+    <td>clustering</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>
+    <td>Task refmap</td>
+    <td></td>
+    <td></td>
+  </tr>
+  <tr>
+    <td>threads_high</td>
+    <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 preprocessed 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>

From 76ba87faee9a5277d664ec017e8f8fcb696b4d4a Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:14:43 +0000
Subject: [PATCH 32/51] Update pipeline_clustering_yml.md

---
 docs/yaml_docs/pipeline_clustering_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index f2b73c37..33bbf38f 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
 
 - <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires. 
+Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires. 
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From e7e33eda94b007b45c3373e6d59acc865b663ee9 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:15:34 +0000
Subject: [PATCH 33/51] Update pipeline_ingestion_yml.md

---
 docs/yaml_docs/pipeline_ingestion_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
index cd1dd293..74b45452 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs,  check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs,  check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 8c5605279992dafacb99e1f095d9f9b1ca9e2660 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:15:55 +0000
Subject: [PATCH 34/51] Update pipeline_integration_yml.md

---
 docs/yaml_docs/pipeline_integration_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md
index 50f63497..7d381a3a 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs. Check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
    Number of threads used for high intensity computing tasks. 

From 8af5044c42e4894e426f821883d91c57d8f484b0 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:16:15 +0000
Subject: [PATCH 35/51] Update pipeline_preprocess_yml.md

---
 docs/yaml_docs/pipeline_preprocess_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md
index 3ecf79cf..413ca353 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md)) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From 080e5134af04a9882e8cf21b078a56e877eeee11 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:16:35 +0000
Subject: [PATCH 36/51] Update pipeline_refmap_yml.md

---
 docs/yaml_docs/pipeline_refmap_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_refmap_yml.md b/docs/yaml_docs/pipeline_refmap_yml.md
index 3a98d6f9..4f1f8af9 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
 Number of threads used for high intensity computing tasks. 

From b9595c1fd5c23be12fda1ee640e6617a45d3ad45 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:17:17 +0000
Subject: [PATCH 37/51] Update pipeline_refmap_yml.md

---
 docs/yaml_docs/pipeline_refmap_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_refmap_yml.md b/docs/yaml_docs/pipeline_refmap_yml.md
index 4f1f8af9..cf6b8c11 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
 Number of threads used for high intensity computing tasks. 

From 1801d8df462c5f7ebf7e4f69994656b40e557759 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:17:39 +0000
Subject: [PATCH 38/51] Update pipeline_preprocess_yml.md

---
 docs/yaml_docs/pipeline_preprocess_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md
index 413ca353..4cbc3293 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md)) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md)) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From 527f586a71b6003f98baae063a515ebf9edc65e3 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:18:03 +0000
Subject: [PATCH 39/51] Update pipeline_preprocess_yml.md

---
 docs/yaml_docs/pipeline_preprocess_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_preprocess_yml.md b/docs/yaml_docs/pipeline_preprocess_yml.md
index 4cbc3293..46ef6bd0 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md)) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         Number of threads used for high intensity computing tasks. 

From f0a5e81ecb5848f4ff035b0a0af2146b051202df Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:18:40 +0000
Subject: [PATCH 40/51] Update pipeline_integration_yml.md

---
 docs/yaml_docs/pipeline_integration_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_integration_yml.md b/docs/yaml_docs/pipeline_integration_yml.md
index 7d381a3a..9b19d4ac 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
    Number of threads used for high intensity computing tasks. 

From 5c4fb23c88ed83557e5299124120b0b16b3b1cb7 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:19:15 +0000
Subject: [PATCH 41/51] Update pipeline_ingestion_yml.md

---
 docs/yaml_docs/pipeline_ingestion_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
index 74b45452..4b1fe645 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs,  check threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 80c1f8714e02c1ad15e71560ad79d2cc355cceaa Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:20:00 +0000
Subject: [PATCH 42/51] Update pipeline_visualization_yml.md

---
 docs/yaml_docs/pipeline_visualization_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_visualization_yml.md b/docs/yaml_docs/pipeline_visualization_yml.md
index 278143b9..e77fdc5c 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
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 579349bee3f4cd1e833344ec895dcbb99854ce24 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:20:36 +0000
Subject: [PATCH 43/51] Update spatial_deconvolution.md

---
 docs/yaml_docs/spatial_deconvolution.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_deconvolution.md b/docs/yaml_docs/spatial_deconvolution.md
index 1e876ee2..acd91c0a 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 8b7ad9c3ac38667dc6ed02941dcc0f123a499442 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:21:02 +0000
Subject: [PATCH 44/51] Update spatial_preprocess.md

---
 docs/yaml_docs/spatial_preprocess.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_preprocess.md b/docs/yaml_docs/spatial_preprocess.md
index 8575d199..84ee8288 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 606026e2c6e982a5b28340275ec4d7790797bb87 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:21:32 +0000
Subject: [PATCH 45/51] Update spatial_qc.md

---
 docs/yaml_docs/spatial_qc.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/spatial_qc.md b/docs/yaml_docs/spatial_qc.md
index 3081a025..4f440b75 100644
--- a/docs/yaml_docs/spatial_qc.md
+++ b/docs/yaml_docs/spatial_qc.md
@@ -28,7 +28,7 @@ For more information on functionalities implemented in `panpipes` to read the co
 
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  check [threads_tasks_panpipes.csv](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.csv) for more information on which threads each specific task requires.
+Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
 Specified by the following three parameters:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From b43a838ad33c650e099e2b4a9de31f1b1c5733c0 Mon Sep 17 00:00:00 2001
From: Fabiola Curion <fabiola.curion@gmail.com>
Date: Wed, 4 Dec 2024 10:17:25 +0100
Subject: [PATCH 46/51] Update threads_tasks_panpipes.md

fix typo
---
 docs/yaml_docs/threads_tasks_panpipes.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/threads_tasks_panpipes.md b/docs/yaml_docs/threads_tasks_panpipes.md
index 185faecb..4d9deaea 100644
--- a/docs/yaml_docs/threads_tasks_panpipes.md
+++ b/docs/yaml_docs/threads_tasks_panpipes.md
@@ -33,7 +33,7 @@
     <td></td>
   </tr>
   <tr>
-    <th colspan="3">Task preprocessed</th>
+    <th colspan="3">Task preprocess</th>
   </tr>
   <tr>
     <th>threads_high</th>

From 5c6b5c4412da7cb3b7e3e78ab8652b667fc9d87d Mon Sep 17 00:00:00 2001
From: bio-la <fabiola.curion@gmail.com>
Date: Wed, 4 Dec 2024 10:41:36 +0100
Subject: [PATCH 47/51] fixed errors

---
 docs/yaml_docs/threads_tasks_panpipes.md | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/docs/yaml_docs/threads_tasks_panpipes.md b/docs/yaml_docs/threads_tasks_panpipes.md
index 4d9deaea..a89e4745 100644
--- a/docs/yaml_docs/threads_tasks_panpipes.md
+++ b/docs/yaml_docs/threads_tasks_panpipes.md
@@ -37,18 +37,20 @@
   </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>threads_low</td>
+    <td>filter_mudata</td>
   </tr>
   <tr>
     <td>rna_preprocess</td>
     <td></td>
-    <td>filter_mudata</td>
+    <td>downsample</td>
   </tr>
   <tr>
     <td>prot_preprocess</td>
@@ -58,7 +60,7 @@
   <tr>
     <td>atac_preprocess</td>
     <td></td>
-    <td>downsample</td>
+    <td></td>
   </tr>
   <tr>
     <th colspan="3">Task integration</th>
@@ -169,12 +171,12 @@
   <tr>
     <td>run_neighbors</td>
     <td>run_clustering</td>
-    <td>clustering</td>
+    <td>plot_clustree</td>
   </tr>
   <tr>
     <td>run_umap</td>
     <td>collate_mdata</td>
-    <td>clustering</td>
+    <td>aggregate_clusters</td>
   </tr>
   <tr>
     <td>find_markers</td>
@@ -220,12 +222,11 @@
     <td></td>
   </tr>
   <tr>
-    <td>Task refmap</td>
-    <td></td>
-    <td></td>
+    <th colspan = "3"> Task refmap </th>
   </tr>
   <tr>
-    <td>threads_high</td>
+    <th>threads_high</th>
+    <th><th>
     <td></td>
     <td></td>
   </tr>
@@ -240,7 +241,7 @@
     <td></td>
   </tr>
   <tr>
-    <th colspan="3">Task preprocessed spatial</th>
+    <th colspan="3">Task preprocess spatial</th>
   </tr>
   <tr>
     <th>threads_high</th>

From 5cbefaf79ceffd1e6212e754988c3288e9a3478e Mon Sep 17 00:00:00 2001
From: bio-la <fabiola.curion@gmail.com>
Date: Wed, 4 Dec 2024 10:48:46 +0100
Subject: [PATCH 48/51] fixed path to table

---
 docs/yaml_docs/pipeline_clustering_yml.md    | 2 +-
 docs/yaml_docs/pipeline_ingestion_yml.md     | 2 +-
 docs/yaml_docs/pipeline_integration_yml.md   | 2 +-
 docs/yaml_docs/pipeline_preprocess_yml.md    | 2 +-
 docs/yaml_docs/pipeline_refmap_yml.md        | 2 +-
 docs/yaml_docs/pipeline_visualization_yml.md | 2 +-
 docs/yaml_docs/spatial_deconvolution.md      | 2 +-
 docs/yaml_docs/spatial_preprocess.md         | 2 +-
 docs/yaml_docs/spatial_qc.md                 | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 33bbf38f..83a7ae2c 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
 
 - <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs, check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires. 
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         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 4b1fe645..fecccada 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 9b19d4ac..4abd27c3 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs. Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
    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 46ef6bd0..50a1ee5a 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         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 cf6b8c11..1ebb0e23 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
 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 e77fdc5c..179f3c03 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
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 acd91c0a..66ba2c44 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 84ee8288..87dbcef4 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
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 4f440b75..51fc1754 100644
--- a/docs/yaml_docs/spatial_qc.md
+++ b/docs/yaml_docs/spatial_qc.md
@@ -28,7 +28,7 @@ For more information on functionalities implemented in `panpipes` to read the co
 
 
 <span class="parameter">resources</span><br>
-Computing resources to use, specifically the number of threads used for parallel jobs.  Check [threads_tasks_panpipes.md](https://github.com/DendrouLab/panpipes/blob/threads_doc_g/docs/yaml_docs/threads_tasks_panpipes.md) for more information on which threads each specific task requires.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 771a7eee59edd9c87d7561c2a77cd25ded194309 Mon Sep 17 00:00:00 2001
From: bio-la <fabiola.curion@gmail.com>
Date: Wed, 4 Dec 2024 10:59:18 +0100
Subject: [PATCH 49/51] added title

---
 docs/yaml_docs/threads_tasks_panpipes.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/yaml_docs/threads_tasks_panpipes.md b/docs/yaml_docs/threads_tasks_panpipes.md
index a89e4745..72c90956 100644
--- a/docs/yaml_docs/threads_tasks_panpipes.md
+++ b/docs/yaml_docs/threads_tasks_panpipes.md
@@ -1,3 +1,5 @@
+# Threads for individual workflow tasks 
+
 <table>
   <tr>
     <th colspan="3">Task ingest</th>

From 4caff3971d32a74a1fe42ade14a86c4775abfa7a Mon Sep 17 00:00:00 2001
From: bio-la <fabiola.curion@gmail.com>
Date: Wed, 4 Dec 2024 11:05:33 +0100
Subject: [PATCH 50/51] paths

---
 docs/yaml_docs/pipeline_clustering_yml.md    | 2 +-
 docs/yaml_docs/pipeline_ingestion_yml.md     | 2 +-
 docs/yaml_docs/pipeline_integration_yml.md   | 2 +-
 docs/yaml_docs/pipeline_preprocess_yml.md    | 2 +-
 docs/yaml_docs/pipeline_refmap_yml.md        | 2 +-
 docs/yaml_docs/pipeline_visualization_yml.md | 2 +-
 docs/yaml_docs/spatial_deconvolution.md      | 2 +-
 docs/yaml_docs/spatial_preprocess.md         | 2 +-
 docs/yaml_docs/spatial_qc.md                 | 3 ++-
 9 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/docs/yaml_docs/pipeline_clustering_yml.md b/docs/yaml_docs/pipeline_clustering_yml.md
index 83a7ae2c..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
 
 - <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         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 fecccada..8aa7eb19 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
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 4abd27c3..1ed0dda0 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
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
    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 50a1ee5a..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
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 2<br>
         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 1ebb0e23..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
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
 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 179f3c03..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
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 66ba2c44..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
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 87dbcef4..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
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         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 51fc1754..5ccbac7a 100644
--- a/docs/yaml_docs/spatial_qc.md
+++ b/docs/yaml_docs/spatial_qc.md
@@ -28,7 +28,8 @@ For more information on functionalities implemented in `panpipes` to read the co
 
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks. 

From 004eb5b595a450af2d93aafb06ae2489066d767a Mon Sep 17 00:00:00 2001
From: bio-la <fabiola.curion@gmail.com>
Date: Wed, 4 Dec 2024 11:12:27 +0100
Subject: [PATCH 51/51] space

---
 docs/yaml_docs/pipeline_ingestion_yml.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
index 8aa7eb19..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
 
 <span class="parameter">resources</span><br>
-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.
+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:
   - <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
         Number of threads used for high intensity computing tasks.