Key concepts and tools

  • stub block, -stub flag
  • ext.args, task.ext.args ?: ''
  • withName: process selector in nextflow.config
  • -with-report, -with-timeline, -with-dag
  • nextflow log, -f fields, -filter expressions
  • .command.sh, .command.err, .exitcode in the work directory
  • nextflow lint, nf-core lint, nextflow inspect
  • nextflow fmt

This lab focuses on the development and debugging features that make Nextflow practical to use on real pipelines. Working with a pre-built FastQC → fastp → MultiQC workflow, you will run the pipeline in stub mode to test channel logic without executing real tools, configure per-tool flags through ext.args in the config file, generate HTML execution reports and timelines, and use nextflow log to locate work directories and read the exact commands that were run. A final section covers linting and formatting tools that catch mistakes before a job is submitted.

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