Merge pull request #78 from DendrouLab/fc_docs

Fc docs

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 out [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/) and 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

docs/install.md

@@ -155,9 +155,14 @@ If using conda environments, you can use one single big environment (the instruc
 The environment (s) should be specified in the .cgat.yml global configuration file or in each of the single workflows pipeline.yml configuration files and it will be picked up by the pipeline as the default environment. 
 Please note that if you specify the conda environment in the workflows configuration file this will be the first choice to run the pipeline. 
 
+On some machines, you may find that `panpipes` is not picking up the correct conda env even if launching the command from a shell where this environment is active. 
+This is normal conda behaviour and documented [here](https://github.com/conda/conda/issues/9392#issuecomment-1291041085). 
+To let the pipeline pick up the right enviornment, run `conda config --set auto_activate_base false`
 
+(or add `auto_activate_base: false` to your .condarc file)
 
-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.
+
+We recommend to add the conda environment param in the .cgat.yml file or in each of the pipeline.yml independently.
 
 i.e. :