Merge pull request #170 from DendrouLab/fc_docs

added index page
DendrouLab · Feb 9, 2024 · b2d84ff · b2d84ff
2 parents dabf8b6 + bb09a7c
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diff --git a/docs/index.rst b/docs/index.rst
@@ -51,6 +51,7 @@ Contents
    install
    usage/index
    workflows/index
+   yaml_docs/index
    tutorials/index
    ../changelog
    contribute_guidelines

diff --git a/docs/yaml_docs/index.rst b/docs/yaml_docs/index.rst
@@ -0,0 +1,10 @@
+Workflows configuration files
+=============================
+
+.. toctree::
+    :maxdepth: 1
+
+    pipeline_ingestion_yml
+    spatial_qc
+    spatial_preprocess
+    spatial_deconvolution
diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md
@@ -8,7 +8,10 @@
   }
 </style>
 
-# pipeline.yml for ingestion workflow
+# Ingestion YAML
+
+In this documentation, the parameters of the `ingest` configuration yaml file are explained. 
+This file is generated running `panpipes ingest config`.  <br> The individual steps run by the pipeline are described in the [spatial preprocess workflow](../workflows/qc.md). 
 
 ## Compute resources options
 

diff --git a/docs/yaml_docs/spatial_deconvolution.md b/docs/yaml_docs/spatial_deconvolution.md
@@ -1,7 +1,9 @@
 
 # Spatial Deconvolution YAML
 
-In this documentation, the parameters of the `deconvolution_spatial` yaml file are explained. In general, the user can leave parameters empty to use defaults. <br> The individual steps run by the pipeline are described in the [spatial deconvolution workflow](../workflows/deconvolute_spatial.md). 
+In this documentation, the parameters of the `deconvolution_spatial` yaml file are explained. 
+This file is generated running `panpipes deconvolution config`.
+In general, the user can leave parameters empty to use defaults. <br> The individual steps run by the pipeline are described in the [spatial deconvolution workflow](../workflows/deconvolute_spatial.md). 
 
 
 

diff --git a/docs/yaml_docs/spatial_preprocess.md b/docs/yaml_docs/spatial_preprocess.md
@@ -1,7 +1,8 @@
 
 # Spatial Preprocessing YAML
 
-In this documentation, the parameters of the `preprocess_spatial` yaml file are explained. In general, the user can leave parameters empty to use defaults. <br> The individual steps run by the pipeline are described in the [spatial preprocess workflow](../workflows/preprocess_spatial.md). 
+In this documentation, the parameters of the `preprocess_spatial` yaml file are explained. 
+This file is generated running `panpipes preprocess_spatial config`. In general, the user can leave parameters empty to use defaults. <br> The individual steps run by the pipeline are described in the [spatial preprocess workflow](../workflows/preprocess_spatial.md). 
 
 
 

diff --git a/docs/yaml_docs/spatial_qc.md b/docs/yaml_docs/spatial_qc.md
@@ -1,7 +1,9 @@
 
 # Spatial QC YAML 
 
-In this documentation, the parameters of the `qc_spatial` yaml file are explained. In general, the user can leave parameters empty to use defaults. <br>  The individual steps run by the pipeline are described in the [spatial QC workflow](../workflows/ingest_spatial.md). 
+In this documentation, the parameters of the `qc_spatial` yaml file are explained. 
+This file is generated running `panpipes qc_spatial config`.
+In general, the user can leave parameters empty to use defaults. <br>  The individual steps run by the pipeline are described in the [spatial QC workflow](../workflows/ingest_spatial.md).