diff --git a/README.md b/README.md index a8349ff..12b0725 100644 --- a/README.md +++ b/README.md @@ -21,19 +21,18 @@ git clone https://github.com/sinanugur/scrna-workflow.git cd scrna-workflow mamba env create --name scrna-workflow --file environment.yml conda activate scrna-workflow - -mamba env create --name cellsnake_testing --file environment.yml ``` For Apple Silicon (i.e. M1, M2 etc.) architecture, you have to put CONDA_SUBDIR=osx-64 before creating the environment. ``` CONDA_SUBDIR=osx-64 mamba env create --name scrna-workflow --file environment.yml +conda activate scrna-workflow ``` -After the environent created and activated, to install required R packages: +After the environment created and activated successfully, to install all the required R packages, you should run the installation script, this may take some time: ``` -./install_r_packages.sh +bash install_r_packages.sh ``` @@ -51,21 +50,16 @@ Then we can run integration. snakemake -j 10 --config option=integration ``` -Now it is time to work on the integrated sample. We can run full advanced run on the integrated object which is always generates at the same location. +Now it is time to work on the integrated sample. We can run standard workflow on the integrated object which is always generates at the same location. ```shell -snakemake -j 10 --config datafolder=analyses_integrated/seurat/integrated.rds resolution=0.3 option=advanced is_integrated_sample=True --rerun-incomplete +snakemake -j 10 --config datafolder=analyses_integrated/seurat/integrated.rds option=standard is_integrated_sample=True --rerun-incomplete ``` +You may change some of the options or you may provide a config file as well, for example. +```shell +snakemake -j 10 --config datafolder=analyses_integrated/seurat/integrated.rds option=standard is_integrated_sample=True --configfile=config.yaml --rerun-incomplete +``` -Do a dry run: -``` -snakemake -j 5 -n -``` - -Show command line arguments and dry run: -``` -snakemake -j 5 -n -p -```