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nf-irida

A Nextflow workflow for generating sample sheets from IRIDA projects at QIB by linking sample metadata with their corresponding files.

Overview

This workflow connects to an IRIDA instance, retrieves sample information for specified projects, and generates CSV sample sheets containing sample names and their associated FASTQ files. It supports processing single or multiple projects and optionally merging results into a single sample sheet.

Prerequisites

  • Nextflow (>=24.04.0)
  • One of the following:
    • Docker or Singularity for container execution
    • Conda for environment management
  • Access to an IRIDA instance with valid credentials

Authentication

The workflow requires IRIDA credentials for authentication. These can be provided through an environment variable. See conf/env.config.example for more details.

The irida.conf format is as follows:

[Settings]
client_id = UPDATE_ME
client_secret = UPDATE_ME
username = UPDATE_ME
password = UPDATE_ME
base_url = UPDATE_ME

Usage

Single project

nextflow run -c conf/env.config \
thanhleviet/nf-irida \
    --project "123" \
    --email "admin@example.com" \
    --outdir "results" \
    -profile conda

Multiple projects

nextflow run -c conf/env.config \
thanhleviet/nf-irida \
    --project "123,456,789" \
    --email "admin@example.com" \
    --outdir "results" \
    --merge true \
    -profile conda

Parameters

  • project: The ID of the IRIDA project to link samples from.
  • email: The email address of the user.
  • outdir: The directory to save the output sample sheet.
  • merge: If true, merge results into a single sample sheet.

Output

The output is a CSV file containing sample names and their associated FASTQ files.

sample_id,fastq1,fastq2
sample1,file1_R1.fastq.gz,file1_R2.fastq.gz
sample2,file2_R1.fastq.gz,file2_R2.fastq.gz
sample3,file3_R1.fastq.gz,file3_R2.fastq.gz

Contributors