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
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
| Nextflow parameter name | Type | Description | Help | Default |
|---|---|---|---|---|
| fastq | string | FASTQ files to use in the analysis. | This accepts one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second case, a sample name can be supplied with --sample. In the last case, 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. |
|
| bam | string | BAM or unaligned BAM (uBAM) files to use in the analysis. | This accepts one of three cases: (i) the path to a single BAM file; (ii) the path to a top-level directory containing BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain BAM files. In the first and second case, a sample name can be supplied with --sample. In the last case, 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. |
|
| analyse_unclassified | boolean | Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified directory. | If selected and if the input is a multiplex directory the workflow will also process the unclassified directory. | False |
| watch_path | boolean | Enable to continuously watch the input directory for new input files. | This option enables the use of Nextflow’s directory watching feature to constantly monitor input directories for new files. | False |
| fastq_chunk | integer | Sets the maximum number of reads per chunk returned from the data ingress layer. | Default is to not chunk data and return a single FASTQ file. |
| Nextflow parameter name | Type | Description | Help | Default |
|---|---|---|---|---|
| sample_sheet | string | A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a directory containing sub-directories with FASTQ files. | The sample sheet is a CSV file with, minimally, columns named barcode and alias. Extra columns are allowed. A type column is required for certain workflows and should have the following values; test_sample, positive_control, negative_control, no_template_control. An optional analysis_group column is used by some workflows to combine the results of multiple samples. If the analysis_group column is present, it needs to contain a value for each sample. |
|
| sample | string | A single sample name for non-multiplexed data. Permissible if passing a single .fastq(.gz) file or directory of .fastq(.gz) files. |
| Nextflow parameter name | Type | Description | Help | Default |
|---|---|---|---|---|
| out_dir | string | Directory for output of all workflow results. | output |
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 }}.
| Title | File path | Description | Per sample or aggregated |
|---|---|---|---|
| workflow report | ./wf-template-report.html | Report for all samples | aggregated |
| Per file read stats | ./fastq_ingress_results/reads/fastcat_stats/per-file-stats.tsv | A TSV with per file read stats, including all samples. | aggregated |
| Per read stats | ./fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
| Run ID's | ./fastq_ingress_results/reads/fastcat_stats/run_ids | List of run ID's present in reads. | aggregated |
| Meta map json | ./fastq_ingress_results/reads/metamap.json | Meta data used in workflow presented in a JSON. | aggregated |
| Concatenated sequence data | ./fastq_ingress_results/reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one fastq file. | per-sample |
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.
See the EPI2ME website for lots of other resources and blog posts.