What are topic channels

Say goodbye to writing a version.yml for each module and mixing the channels together. To improve here, we will be adopting topic channels. Topic channels can collect values from multiple sources automatically, just by sharing the same topic name. This means no more tangled channel wiring or mix operator chains. With topic channels, you can now broadcast and collect data across your pipeline more naturally.

process  {
  output:
  val('hello'), topic: my_topic
 
  // ...
}
 
process bye {
  output:
  val('bye'), topic: my_topic
 
  // ...
}

See also the channels documention and the migration tutorial

How to adopt your module

Let’s get to work. Grab any nf-core module

1. Adapt main.nf

No need to write to version.yml files any more, we emit a topic channel in the output section instead.

output:
tuple val(meta), path("*.html"), emit: html
tuple val(meta), path("*.zip") , emit: zip
-path  "versions.yml"           , emit: versions
+tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions
︙
-cat <<-END_VERSIONS > versions.yml
-"${task.process}":
-    fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-END_VERSIONS

2. Semi-automatic meta.yml update

Update the meta.yml using nf-core/tools. Then fill in the version information.
You can update the meta.yml conveniently using
nf-core modules lint <MODULE_NAME> --fix

  versions_fastqc:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - fastqc:
          type: string
          description: The tool name
      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
          type: string
          description: The command used to generate the version of the tool
topics:
  - versions:
      - - process:
            type: string
            description: The process the versions were collected from
        - tool:
            type: string
            description: The tool name
        - version:
            type: string
            description: The version of the tool

3. Catch version in tests/main.nf.test

This might be a little more tricky for some of your modules, but a good start to catch the version in the snapshot is:

process.out.findAll { key, val -> key.startsWith("versions")}

4. Update snapshot

As no version.yml exists anymore, you will have to update the snapshot.

5. Fix dependent nf-core/subworkflows

All nf-core/subworkflows which are calling your module will fail now because no version.yml is created to use the mix operator on. So, you should remove all occurences of:

ch_versions = ch_versions.mix(FASTQC.out.versions.first())

Make sure to update the snapshots of the subworkflows as well.

Published on

6 November 2025

Written by

@mapo9

@nvnieuwk

@mribeirodantas

@kobelavaerts

@wangdepin

@yadavbha

@eit-maxlcummins