Nextflow workflow template repository.

This workflow is not intended to be used by end users.

This workflow can be used for the following:

• As a template using gitlabs create project from template.
• For testing of any scripts that are the same across workflows such as scripts in the lib directory.

Recommended requirements:

• CPUs = 2
• Memory = 2GB

Minimum requirements:

• CPUs = 2
• Memory = 2GB

Approximate run time: 5 minutes per sample

ARM processor support: True

These are instructions to install and run the workflow on command line. You can also access the workflow via the EPI2ME Desktop application.

The workflow uses Nextflow to manage compute and software resources, therefore Nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either [Docker](https://www.docker.com/products/docker-desktop or Singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either Docker or Singularity is installed. This is controlled by the -profile parameter as exemplified below.

It is not required to clone or download the git repository in order to run the workflow. More information on running EPI2ME workflows can be found on our website.

The following command can be used to obtain the workflow. This will pull the repository in to the assets folder of Nextflow and provide a list of all parameters available for the workflow as well as an example command:

nextflow run epi2me-labs/wf-template --help

To update a workflow to the latest version on the command line use the following command:

nextflow pull epi2me-labs/wf-template

A demo dataset is provided for testing of the workflow. It can be downloaded and unpacked using the following commands:

wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-template/wf-template-demo.tar.gz
tar -xzvf wf-template-demo.tar.gz

The workflow can then be run with the downloaded demo data using:

nextflow run epi2me-labs/wf-template \
	--fastq 'wf-template-demo/test_data/reads.fastq.gz' \
	-profile standard

For further information about running a workflow on the command line see https://labs.epi2me.io/wfquickstart/

This workflow is designed to take input sequences that have been produced from Oxford Nanopore Technologies devices.

Find related protocols in the Nanopore community.

This workflow accepts either FASTQ or BAM files as input.

The FASTQ or BAM input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ or BAM file; (ii) the path to a top-level directory containing FASTQ or BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ or BAM files. In the first and second cases (i and ii), a sample name can be supplied with --sample. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with --sample_sheet.

(i)                     (ii)                 (iii)    
input_reads.fastq   ─── input_directory  ─── input_directory
                        ├── reads0.fastq     ├── barcode01
                        └── reads1.fastq     │   ├── reads0.fastq
                                             │   └── reads1.fastq
                                             ├── barcode02
                                             │   ├── reads0.fastq
                                             │   ├── reads1.fastq
                                             │   └── reads2.fastq
                                             └── barcode03
                                              └── reads0.fastq

Output files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.

The fastcat/bamstats tool is used to concatenate multifile samples to be processed by the workflow. It will also output per read stats including average read lengths and qualities.

• If the workflow fails please run it with the demo data set to ensure the workflow itself is working. This will help us determine if the issue is related to the environment, input parameters or a bug.
• See how to interpret some common nextflow exit codes here.

If your question is not answered here, please report any issues or suggestions on the github issues page or start a discussion on the community.

• Importing third-party workflows into EPI2ME Labs

See the EPI2ME website for lots of other resources and blog posts.