diff --git a/README.md b/README.md index ed24e63..31fc58b 100644 --- a/README.md +++ b/README.md @@ -18,8 +18,8 @@ The workflow can currently be run using either the required software. Both methods are automated out-of-the-box provided either docker of conda is installed. -> See the sections below for installation of these prerequisites in various scenarios. -> It is not required to clone or download the git repository in order to run the workflow. +It is not required to clone or download the git repository in order to run the workflow. +For more information on running EPI2ME Labs workflows [visit out website](https://labs.epi2me.io/wfindex). **Workflow options** @@ -39,192 +39,6 @@ The primary outputs of the workflow include: * an HTML report document detailing the primary findings of the workflow. -### Supported installations and GridION devices - -Installation of the software on a GridION can be performed using the command - -`sudo apt install ont-nextflow` - -This will install a java runtime, Nextflow and docker. If *docker* has not already been -configured the command below can be used to provide user access to the *docker* -services. Please logout of your computer after this command has been typed. - -`sudo usermod -aG docker $USER` - -### Installation on Ubuntu devices - -For hardware running Ubuntu the following instructions should suffice to install -Nextflow and Docker in order to run the workflow. - -1. Install a Jva runtime environment (JRE): - - ```sudo apt install default-jre``` - -2. Download and install Nextflow may be downloaded from https://www.nextflow.io: - - ```curl -s https://get.nextflow.io | bash``` - - This will place a `nextflow` binary in the current working directory, you - may wish to move this to a location where it is always accessible, e.g: - - ```sudo mv nextflow /usr/local/bin``` - -3. Install docker and add the current user to the docker group to enable access: - - ``` - sudo apt install docker.io - sudo usermod -aG docker $USER - ``` - -## Running the workflow - -The `wf-template` workflow can be controlled by the following parameters. The `fastq` parameter -is the most important parameter: it is required to identify the location of the -sequence files to be analysed. - -**Parameters:** - -- `fastq` specifies a *directory* path to FASTQ files (required) -- `out_dir` the path for the output (default: output) - -To run the workflow using Docker containers supply the `-profile standard` -argument to `nextflow run`: - -> The command below uses test data available from the [github repository](https://github.com/epi2me-labs/wf-template/tree/master/test_data) -> It can be obtained with `git clone https://github.com/epi2me-labs/wf-template`. - -``` -# run the pipeline with the test data -OUTPUT=output -nextflow run epi2me-labs/wf-template \ - -w ${OUTPUT}/workspace \ - -profile standard \ - --fastq test_data \ - --out_dir ${OUTPUT} -``` - -The output of the pipeline will be found in `./output` for the above -example. This directory contains the nextflow working directories alongside -the two primary outputs of the pipeline: a `seqs.txt` file containing a summary -of all reads, and a `report.html` file summarising the workflows calculations. - -### Running the workflow with Conda - -To run the workflow using conda rather than docker, simply replace - - -profile standard - -with - - -profile conda - -in the command above. - -### Configuration and tuning - -> This section provides some minimal guidance for changing common options, see -> the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for further details. - -The default settings for the workflow are described in the configuration file `nextflow.config` -found within the git repository. The default configuration defines an *executor* that will -use a specified maximum CPU cores (four at the time of writing) and RAM (eight gigabytes). - -If the workflow is being run on a device other than a GridION, the available memory and -number of CPUs may be adjusted to the available number of CPU cores. This can be done by -creating a file `my_config.cfg` in the working directory with the following contents: - -``` -executor { - $local { - cpus = 4 - memory = "8 GB" - } -} -``` - -and running the workflow providing the `-c` (config) option, e.g.: - -``` -# run the pipeline with custom configuration -nextflow run epi2me-labs/wf-template \ - -c my_config.cfg \ - ... -``` - -The contents of the `my_config.cfg` file will override the contents of the default -configuration file. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) -for more information concerning customized configuration. - -**Using a fixed conda environment** - -By default, Nextflow will attempt to create a fresh conda environment for any new -analysis (for reasons of reproducibility). This may be undesirable if many analyses -are being run. To avoid the situation a fixed conda environment can be used for all -analyses by creating a custom config with the following stanza: - -``` -profiles { - // profile using conda environments rather than docker - // containers - fixed_conda { - docker { - enabled = false - } - process { - withLabel:artic { - conda = "/path/to/my/conda/environment" - } - shell = ['/bin/bash', '-euo', 'pipefail'] - } - } -} -``` - -and running nextflow by setting the profile to `fixed_conda`: - -``` -nextflow run epi2me-labs/wf-template \ - -c my_config.cfg \ - -profile fixed_conda \ - ... -``` - -## Updating the workflow - -Periodically when running the workflow, users may find that a message is displayed -indicating that an update to the workflow is available. - -To update the workflow simply run: - - nextflow pull epi2me-labs/wf-template - -## Building the docker container from source - -The docker image used for running the `wf-template` workflow is available on -[dockerhub](https://hub.docker.com/repository/docker/ontresearch/wf-template). -The image is built from the Dockerfile present in the git repository. Users -wishing to modify and build the image can do so with: - -``` -CONTAINER_TAG=ontresearch/wf-template:latest - -git clone https://github.com/epi2me-labs/wf-template -cd wf-template - -docker build \ - -t ${CONTAINER_TAG} -f Dockerfile \ - --build-arg BASEIMAGE=ontresearch/base-workflow-image:v0.1.0 \ - . -``` - -In order to run the workflow with this new image it is required to give -`nextflow` the `--wfversion` parameter: - -``` -nextflow run epi2me-labs/wf-template \ - --wfversion latest -``` - ## Useful links * [nextflow](https://www.nextflow.io/)