A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

How to handle the case where a tool simply returns a single value and nothing else? (to stdout)

<https://docs.seqera.io/nextflow/process#standard-output-stdout>

No, I think I worded my request wrongly: I mean, I want to store it somewhere (so it can be collected at the end of whatever workflow is used), but the tool just spits out this value and nothing else

You can use `eval` and handle it like we do the versions?

Oh, right, my idea was to wrap it somewhow with `meta.id` so I can have the sample and the associated value

you can use the `stdout` option, then read it and add it to `meta` using `map`

Because this is omething I want to make a PR for

Nothing stopping you from using `stdout` if you’re just going to read the value anyway

saves you the code for writing and reading

```process stdoutprocess {
    input:
    tuple val(meta), path(whatever)

    output:
    tuple val(meta), stdout, emit: results

    script:
    """
    tool --input $whatever
    """
}

workflow {
    stdoutprocess.results.map{ meta, out -&gt; return [meta + [output: out]]}
}```
Or smth like this

Yeah, but I thought it would be better for the end user to have a file with the data and the `meta.id`

so I just piped it into `sed` to prepend `meta.id` then a tab, done.

I don't like `stdout` because it can sometimes pick up noise from other side processes (eg. slurm complaining about something)

If you redirect to a file, you're guaranteed to capture only the stdout _from that tool invocation_, so it's fractionally safer