Question regarding a workflow with multiple outputs

[ekageyama]

I have a workflow where its last step has a process with multiple channels, but when I try to use the output, i get the error:

ERROR ~ Cannot emit a multi-channel output: $out0

the workflow is

workflow test{
    take: sample_qch
    main:
        process1(sample_qch)
    emit:
      process1.out
}

where the process1 has an output like this

        output:
        tuple val(acc), path('filter*')
        path('*.html')
        path('*.json')

the idea behind is that the tuple part will keep being processed by a second workflow, while the json and html file will be used for second and third different workflows. Any help is appreciated

[bentsherman]

Because your process has multiple output channels, process1.out is a multi-channel and cannot be emitted as a workflow output. Instead, you should emit each process output separately in the workflow:

emit:
  process1.out[0]
  process1.out[1]
  process1.out[2]

And of course you can name those outputs and access them by name, and you can select which outputs you want to emit from the workflow.

[colindaven]

I try to avoid tuples for simplicity, but just use name prefixes.

In any event, I write output like this from process1

  output:
   path "*anno.gff3", emit: anno_gff3
   path "*.sum", emit: summary

and if I want to use that output from process1 in another process2 then I use this in the workflow section:

process2(process1.out.anno_gff3, process1.out.summary)