feat-2-0: Unknown config attribute params.fastq

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/clipseq pipeline documentation

Description of the bug

I was running the latest commit f4334d817405b37b18cdf8f03b4211b2d0cb3fbb and have the error described below:

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: run nf-core/clipseq -r feat-2-0 -profile test,docker
2. See error:

N E X T F L O W ~ version 25.10.3

Pulling nf-core/clipseq ... downloaded from https://github.com/nf-core/clipseq.git ERROR ~ Unknown config attribute params.fastq -- check config file: /home/svetlana/.nextflow/assets/nf-core/clipseq/nextflow.config

-- Check '.nextflow.log' file for details

Expected behaviour

Successful test run.

Log files

Have you provided the following extra information/files:

• [x ] The command used to run the pipeline
• The .nextflow.log file

System

• Hardware: local laptop
• Executor: local
• OS: ubuntu
• Version 24.04

Nextflow Installation

• Version: 25.10.3

Container engine

• Engine: docker
• version: Docker version 29.2.1, build a5c7197
• Image tag: nfcore/clipseq:feat-2-0

Additional context

AI thinks that the following line in nextflow.config :

source = fastq // fastq or bam

Should be quoted:

source = 'fastq' // fastq or bam

And this seems to fix the issue for me.

Start by inspecting nextflow.config and reproducing the reported command, run nf-core/clipseq -r feat-2-0 -profile test,docker. Check the source configuration mentioned in the report and confirm that the test profile completes successfully without the unknown params.fastq error.