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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:

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

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

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..)
Compile the plugin along the Nextflow code, with this command:
```
./gradlew assemble
```
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:

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.

The following command, package and upload the plugin in the GitHub project releases page:
```
./gradlew :plugins:nf-ffq:upload
```
Create a pull request against the nextflow-io/plugins project to make the plugin public accessible to Nextflow app.

Releases

Release	Date	Downloads	Author
0.2.0	2024-03-06	168	pditommaso