Add Singularity documentation

README.md

@@ -7,33 +7,41 @@
 [![PGO badge](https://img.shields.io/badge/PathoGenOmics-Lab-yellow.svg)](https://pathogenomics.github.io/)
 [![DOI:10.1101/2023.10.24.561010](https://img.shields.io/badge/DOI-10.1101/2023.10.24.561010-blue.svg)](https://doi.org/10.1101/2023.10.24.561010)
 [![Release](https://img.shields.io/github/v/release/PathoGenOmics-Lab/VIPERA)](https://github.com/PathoGenOmics-Lab/VIPERA/releases)
-[![Snakemake](https://img.shields.io/badge/snakemake-≥7.19-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)
+[![Snakemake](https://img.shields.io/badge/Snakemake-≥7.19-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)
 ![Install workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/install.yml/badge.svg)
 ![Test workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test.yml/badge.svg)
 
 A pipeline for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis.
 
-## Instructions
+## First steps
 
 To run VIPERA locally with the default configuration, you only need one line of code after
 [installing Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html),
 configuring [the inputs and outputs](config/README.md#inputs-and-outputs) and
 [the context dataset](config/README.md#automated-construction-of-a-context-dataset):
 
 ```shell
-snakemake --use-conda -c4  # runs VIPERA on 4 cores (reccomended)
+snakemake --use-conda -c4  # runs VIPERA on 4 cores
 ```
 
-Alternatively, you can use a simple script that downloads the [data](https://doi.org/10.20350/digitalCSIC/15648) from [our study](https://doi.org/10.1101/2023.10.24.561010)
-and performs the analysis in one step:
+We provide a simple script that downloads the [data](https://doi.org/10.20350/digitalCSIC/15648) from [our study](https://doi.org/10.1101/2023.10.24.561010)
+and performs the analysis in a single step:
 
 ```shell
 ./run_default_VIPERA.sh
 ```
 
-This Snakemake workflow can be also [executed in an HPC environment](config/README.md#run-modes).
+This Snakemake workflow is compatible with both local execution and HPC environments utilizing SLURM. It supports dependency management through either conda or Singularity, as detailed in the [run modes documentation](config/README.md#run-modes).
 
-Please refer to [config/README.md](config/README.md) for detailed setup instructions.
+Please refer to the [full workflow documentation](config/README.md) for detailed setup instructions.
+
+> The documentation in this repository provides instructions for running VIPERA
+> with Snakemake <8. We recommend using Snakemake 7.32.
+> However, using Snakemake 8 is possible with minimal modifications (see the
+> [migration documentation](https://snakemake.readthedocs.io/en/stable/getting_started/migration.html)).
+> For example, `--use-conda` and `--use-singularity` are deprecated in Snakemake 8,
+> and `--software-deployment-method conda apptainer` is the preferred way to provide the options. Additionally, SLURM support is only available after installing an
+> [executor plugin for slurm](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html).
 
 ## Contributors
 

config/README.md

@@ -154,7 +154,7 @@ To run the analysis with the default configuration, run the following command
 (change the `-c/--cores` argument to use a different number of CPUs):
 
 ```shell
-snakemake --use-conda -c8
+snakemake --use-conda -c4
 ```
 
 To run the analysis in an HPC environment using SLURM, we provide a
@@ -164,3 +164,10 @@ should be modified to fit your needs. To use it, run the following command:
 ```shell
 snakemake --use-conda --slurm --profile profile/default
 ```
+
+Additionally, we offer the option of running the workflow within a containerized
+environment using a [pre-built Docker image](https://hub.docker.com/r/ahmig/vipera),
+provided that [Singularity](https://en.wikipedia.org/wiki/Singularity_(software))
+is available on the system. This eliminates the need for further conda package
+downloads and environment configuration.
+To do that, simply add the option `--use-singularity` to any of the previous commands.