@@ -13,9 +13,9 @@ If you want to use the pipeline, please follow the following easy instructions:
**For parameter explanation, see the explanations in the config yaml files.**
**There are some important changes that were introduced with the most recent version. Make sure to read the config.yaml and ask Christian in case of open questions. In short, some parameters and parts of the pipeline have been deprecated (Encode peak calling), default paramters have changed (e.g., no RSS adjustment is done anymore by default, but this can be changed).**
**There are some important changes that were introduced with the most recent version. Make sure to read the config.yaml and ask Christian in case of open questions. In short, some parameters and parts of the pipeline have been deprecated (Encode peak calling), default paramters have changed (e.g., no RSS adjustment is done anymore by default, but this can be changed).**
**Currently, there is only one limitation that will be resolved soon: The new Singularity container for R is still missing. Therefore, most R-related rules can currently only be executed without Singularity, which means that you have to have particular packages being pre-installed. Contact Christian if this affects you, this note will be removed once the container is updated properly. Use the following line to install the packages:**
**Currently, there is only one limitation that will be resolved soon: The new Singularity container for R is still missing. Therefore, most R-related rules can currently only be executed without Singularity, which means that you have to have particular packages being pre-installed. Contact Christian if this affects you, this note will be removed once the container is updated properly. Use the following line to install the packages:**
