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 # Workflow template
 
-This repository contains a Nextflow workflow template and associated Docker
-container build. The workflow also supports using conda environments as an
-alternative software isolation method to Docker.
+This repository contains a [nextflow](https://www.nextflow.io/) workflow
+template that can be used as the basis for creating new workflows.
+
+> This workflow is not intended to be used by end users.
+
 
 ## Quickstart
 
-### Building the container
+The workflow uses [nextflow](https://www.nextflow.io/) to manage compute and 
+software resources, as such nextflow will need to be installed before attempting
+to run the workflow.
 
-> This step is not necessary if you intend to run the workflow using
-> conda environments, or are not interesting in developing of modifying
-> the workflow. The current release version of the container is located
-> on dockerhub with the tag ontresearch/wf-template.
+The workflow can currently be run using either
+[Docker](https://www.docker.com/products/docker-desktop) or
+[conda](https://docs.conda.io/en/latest/miniconda.html) to provide isolation of
+the required software. Both methods are automated out-of-the-box provided
+either docker of conda is installed.
 
-The Docker container image can be built with the following command:
+> 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.
 
-```bash
-CONTAINER_TAG=ontresearch/wf-template
-docker build \
-    -t ${CONTAINER_TAG} -f Dockerfile \
-    --build-arg BASEIMAGE=ontresearch/base-workflow-image:v0.1.0 \
-    .
+**Workflow options**
+
+To obtain the workflow, having installed `nextflow`, users can run:
+
+```
+nextflow run epi2me-labs/wf-template --help
 ```
 
-The `BASEIMAGE` argument here can be changed to use an alternative image.
+to see the options for the workflow.
 
-### Running the workflow
+**Workflow outputs**
 
-The template includes a simple workflow that outputs a file with the lengths
-of sequences contained in a .fastq.gz file.
+The primary outputs of the workflow include:
 
-**Running the workflow with Docker containers**
+* a simple text file providing a summary of sequencing reads,
+* 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`.
+
 ```
-OUTPUT=workflow-output
-nextflow run main.nf \
+# run the pipeline with the test data
+OUTPUT=output
+nextflow run epi2me-labs/wf-template \
     -w ${OUTPUT}/workspace \
     -profile standard \
     --fastq test_data/reads.fq.gz \
     --out_dir ${OUTPUT}
 ```
 
-The output of the pipeline will be found in `./workflow-output` for the above
+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.
+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.
 
-**Using conda environments**
+### Running the workflow with Conda
 
-To run the workflow backed by conda environments, simply provide the
-`-profile conda` argument to `nextflow run`.
+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:
 
 ```
-# run the pipeline with the test data
-OUTPUT=workflow-output
-nextflow run main.nf \
-    -w ${OUTPUT}/workspace \
-    -profile conda \
-    --fastq test_data/reads.fq.gz \
-    --out_dir ${OUTPUT}
+executor {
+    $local {
+        cpus = 4
+        memory = "8 GB"
+    }
+}
 ```
 
-This will create a conda environment with all required software within the
-workspace directory. When running multiple analyses on distinct datasets
-it may not be desirable to have Nextflow create a conda environment for each
-analysis. To avoid the situation editing the file `nextflow.config` will
-be necessary. Search for the term `cacheDir` and set this to a directory
-where you wish the conda environment to be placed.
+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/)
+* [docker](https://www.docker.com/products/docker-desktop)
+* [conda](https://docs.conda.io/en/latest/miniconda.html)