nextflow-io / nf-ffq

Nextflow plugin to fetch fastq samples via ffq

nf-ffq

Nextflow plugin to fetch fastq samples using ffq.

Get started

The plugin adds a new channel factory called channel.ffq() which can be used to query fastq files.

Note

This plugin requires Nextflow 24.01.0-edge or later.

A simple usage is shown below:

include { ffq } from 'plugin/nf-ffq'

channel
  .ffq('SRR9990627', filetype: 'fastq', links: 'aws')
  .view()

Run it using this command:

nextflow run <your script name> -plugins nf-ffq

It returns:

[SRR9990627, [s3://sra-pub-src-16/SRR9990627/macula_donor_1_S100_L004_R1_001.fastq.gz.1, s3://sra-pub-src-17/SRR9990627/macula_donor_1_S100_L004_R2_001.fastq.gz.1]]

Options

The ffq method can take either a string value representing an accession ID, a string value representing string representing a comma separate list of accession IDs, or a list of string of accession IDs.

The following options can be specified provided:

Option	Description
filetype	The requested file type, either fastq or sra
links	The link type that should be returned, either aws, gcp, ncbi, ftp

Configuration

The plugin adds a new ffq config scope which supports the following options:

Config option	Description
ffq.endpoint	URL of the ffq-api endpoint

For example:

ffq {
  endpoint = 'https://ffq.seqera.io'
}

Development

Run the following command in the project root directory (ie. where the file settings.gradle is located):

./gradlew check

Run and debug plugin in the development environment

To run and test the plugin in the development environment, configure a local Nextflow build using the following steps:

1. Clone the Nextflow repository in your computer into a sibling directory:

   git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow
   

2. Instruct the plugin build setting to use the local Nextflow code, adding the following line in the file settings.gradle:

   echo "includeBuild('../nextflow')" >> settings.gradle
   

(make sure to not add it more than once..)

3. Compile the plugin along the Nextflow code, with this command:

   ./gradlew assemble
   

4. Run Nextflow with plugins using the ./launch.sh script as a drop-in replacement for the nextflow command and adding the option -plugins nf-ffq to load the built plugin:

   ./launch.sh run ffq.nf -plugins nf-ffq
   

Package, upload and publish

The project should hosted in a GitHub repository whose name should match the name of the plugin, that is the name of the directory in the plugins folder e.g. nf-ffq in this project.

Following these step to package, upload and publish the plugin:

1. Create a file named gradle.properties in the project root containing the following attributes (this file should not be committed in the project repository):

• github_organization: the GitHub organisation the plugin project is hosted
• github_username The GitHub username granting access to the plugin project.
• github_access_token: The GitHub access token required to upload and commit changes in the plugin repository.
• github_commit_email: The email address associated with your GitHub account.

2. The following command, package and upload the plugin in the GitHub project releases page:

   ./gradlew :plugins:nf-ffq:upload
   

3. Create a pull request against the nextflow-io/plugins project to make the plugin public accessible to Nextflow app.

nf-ffq's Issues

Add plugin endpoint

It should be possible to configure the plugin endpoint via the following setting in the nextflow.config file:

ffq {
  endpoint = 'http://something'
} 

It the future it will be used to control more settings. A good pattern to follow is shown below

https://github.com/nextflow-io/nextflow/blob/master/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveConfig.groovy#L28-L47