change the docs

DendrouLab · Aug 31, 2023 · 296872b · 296872b
1 parent 0e8363f
commit 296872b
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/README.md b/README.md
@@ -1,11 +1,11 @@
 # Panpipes - multimodal single cell pipelines 
 
 Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion  
-Additional contributors: Devika Agarwal and Tom Thomas 
+Additional contributors: Sarah Ouologuem, Devika Agarwal and Tom Thomas 
 
 See our [preprint](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v1):  
 Panpipes: a pipeline for multiomic single-cell data analysis  
-Charlotte Rich-Griffin, Fabiola Curion, Tom Thomas, Devika Agarwal, Fabian J. Theis, Calliope A. Dendrou.  
+Charlotte Rich-Griffin*, Fabiola Curion*, Tom Thomas, Devika Agarwal, Fabian J. Theis, Calliope A. Dendrou.  
 bioRxiv 2023.03.11.532085;  
 doi: https://doi.org/10.1101/2023.03.11.532085
 
@@ -20,7 +20,9 @@ Available pipelines:
 4. "clustering" : cell clustering on single modalities
 5. "refmap" : transfer scvi-tools models from published data to your data
 6. "vis" : visualise metrics from other pipelines in context of experiment metadata
-
+7. "qc_spatial": for the ingestion of Spatial Transcriptomics data (vizgen, visium) and computation of QC metrics
+8. "preprocess_spatial" : for filtering and normalising of ST data
+9. "deconvolution": for the cell type deconvolution of ST slides
 
 
 # Installation and configuration

diff --git a/docs/install.md b/docs/install.md
@@ -157,7 +157,10 @@ Please note that if you specify the conda environment in the workflows configura
 
 
 
-If no environment is specified, the default behaviour of the pipeline is to inherit environment variables from the node where the pipeline is run. However there have been reported issues on SLURM clusters where this was not the default behaviour. In those instances we recommend to add the conda environment param in the .cgat.yml file or in each of the pipeline.yml independently.
+If no environment is specified, the default behaviour of the pipeline is to inherit environment variables from the node where the pipeline is run. However there have been reported issues on SLURM clusters where this was not the default behaviour. 
+
+
+We recommend to add the conda environment param in the .cgat.yml file or in each of the pipeline.yml independently.
 
 i.e. :
-Original file line number
+Diff line change
@@ Expand Up @@
-    If no environment is specified, the default behaviour of the pipeline is to inherit environment variables from the node where the pipeline is run. However there have been reported issues on SLURM clusters where this was not the default behaviour. In those instances we recommend to add the conda environment param in the .cgat.yml file or in each of the pipeline.yml independently.
+    If no environment is specified, the default behaviour of the pipeline is to inherit environment variables from the node where the pipeline is run. However there have been reported issues on SLURM clusters where this was not the default behaviour.
+    We recommend to add the conda environment param in the .cgat.yml file or in each of the pipeline.yml independently.
     i.e. :
@@ Expand Down @@