Update pipelines to use topic channels

Adapting pipelines to use topic channels for version outputs is a straightforward process explained in the steps below:

1. Update the template of the pipeline to the latest version that includes support for topic channels (nf-core tools >=3.5.0).

   The main change in the template are the following lines:

     def topic_versions = channel.topic("versions")
         .distinct()
         .branch { entry ->
             versions_file: entry instanceof Path
             versions_tuple: true
         }
     def topic_versions_string = topic_versions.versions_tuple
         .map { process, tool, version ->
             [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
         }
         .groupTuple(by:0)
         .map { process, tool_versions ->
             tool_versions.unique().sort()
             "${process}:\n${tool_versions.join('\n')}"
         }
     ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
         .mix(topic_versions_string)
     ch_collated_versions = softwareVersionsToYAML(ch_versions)

2. Pull the latest changes made to modules using nf-core modules update.

3. Look for issues in the pipeline code where versions is an invalid output of a process. Remove these outputs since these are now handled by the topic channels. The errors will most likely look like this:

   ```console title="nextflow.log"
   ERROR ~ No such variable: Exception evaluating property 'versions' for nextflow.script.ChannelOut,
   Reason: groovy.lang.MissingPropertyException:
   No such property: versions for class: groovyx.gpars.dataflow.DataflowBroadcast
   ```
    
   Example: We just updated the `samtools/sort` module to use topic channels. The pipeline will most likely have something like this in one of the (sub)workflows:
    
   ```groovy title="main.nf"
   SAMTOOLS_SORT(input)
   ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)
   ```
    
   The above error can be fixed by removing the line that references `SAMTOOLS_SORT.out.versions`, as shown below:
    
   ```groovy title="main.nf"
   SAMTOOLS_SORT(input)
   ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) // [!code --]
   ```