diff --git a/README.md b/README.md index bf11dd6..cd4c198 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ The `distiller` pipeline aims to provide the following functionality: Requirements: -- java 7/8 +- java 8 - [nextflow](https://www.nextflow.io/) - docker (should be able to run w/o root privileges, [tutorial](https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-16-04)) @@ -33,13 +33,24 @@ This will download the distiller pipeline and the configuration files. Then: - configure the location of the input files and other project details in `project.yml` -- configure the hardware/system details in `nextflow.config` and/or in `./configs/*.config` +- configure additional parameters in `nextflow.config` +- use provided hardware configurations using `local` and `cluster` profiles, or provide your own using `custom` profile -Launch distiller as: +Launch distiller depending on your usage scenario: +1. default hardware settings `./configs/local.config` with your `project.yml`: ```sh -$ nextflow distiller.nf -params-file project.yml +$ nextflow run distiller.nf -params-file project.yml ``` +2. `cluster` hardware profile `./configs/cluster.config` with your `project.yml`: +```sh +$ nextflow run distiller.nf -params-file project.yml -profile cluster +``` +3. `custom` hardware profile with your own configuration file and your `project.yml`: +```sh +$ nextflow run distiller.nf -params-file project.yml -profile custom --custom_config /full/path/to/your.config +``` + ### Test example