# Variable defined w/ def gives "Missing name with which to set the channel variable"

**URL:** <https://community.seqera.io/t/variable-defined-w-def-gives-missing-name-with-which-to-set-the-channel-variable/582>\
**Category:** Ask for help\
**Created:** [March 21, 2024, 5:03pm UTC](https://community.seqera.io/t/variable-defined-w-def-gives-missing-name-with-which-to-set-the-channel-variable/582 "2024-03-21T17:03:54Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![bskubi](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/bskubi/32/545_2.png) [@bskubi](https://community.seqera.io/u/bskubi)\
**Post date:** [March 21, 2024, 5:03pm UTC](https://community.seqera.io/t/variable-defined-w-def-gives-missing-name-with-which-to-set-the-channel-variable/582/1 "2024-03-21T17:03:54Z")

</div>

```auto
workflow convert_sam_to_bam {
    take:
    genrf_ch

    main:
    // def sam_to_bam_ch = Channel.empty()
    sam_to_bam_ch = Channel.empty()
    if (!params.sam.isBlank())
    {
        channel
            .fromPath(params.sam)
            .map{tuple(string_prefix(it.toString(), "convert_sam_to_bam"), it)}
            .combine(genrf_ch)
            .set{sam_ch}
        

        /*
        sam_to_bam(sam_ch)
            .set{sam_to_bam_ch}
        */
        sam_to_bam_ch = sam_to_bam(sam_ch)
    }
    
    emit:
    sam_to_bam_ch
}

```

In the code above, I get an error if I define `sam_to_bam_ch` with `def`.

When `sam_to_bam_ch` is defined with `def`, within the `if` statement, the statement

```auto
sam_to_bam(sam_ch)
        .set{sam_to_bam_ch}

```

Gives the error

`ERROR ~ Missing name with which to set the channel variable`

The statement

```auto
sam_to_bam_ch = sam_to_bam(sam_ch)

```

Gives the error

`Missing workflow output parameter: sam_to_bam_ch`

The code runs either way if I don’t use `def` to define `sam_to_bam_ch`.

I’d appreciate clarification on a few things:

1. If I don’t use `def` when I define sam\_to\_bam\_ch, will it have global scope?
2. I prefer to keep variable scope local when possible, is there a way to make sam\_to\_bam have local scope (while still being emittable) and get this code to work?
3. Why do the two statements calling `sam_to_bam` produce different error messages?
4. Why does `def sam_to_bam_ch` generate any error message at all in this case? My understanding of Groovy’s scoping is that its scope should extend into the `if` block.

---

<div class="post-metadata">

**Author:** ![mribeirodantas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mribeirodantas/32/235_2.png) [@mribeirodantas](https://community.seqera.io/u/mribeirodantas)\
**Post date:** [March 21, 2024, 5:41pm UTC](https://community.seqera.io/t/variable-defined-w-def-gives-missing-name-with-which-to-set-the-channel-variable/582/2 "2024-03-21T17:41:27Z")

</div>

The scope of variables within the Nextflow process/workflow blocks is a bit unintuitive. There are two community pages that explain a bit about this [here](https://midnighter.github.io/nextflow-gotchas/gotchas/shell-global-only/) and [here](https://midnighter.github.io/nextflow-gotchas/gotchas/variable-scope/).

You will see in the link above that global variables can not be set to local variables. That’s what you’re doing when you get the output channel from the `sam_to_bom` process and try to assign to `sam_to_bam_ch` that was created with `def`. It’s not related to inside or outside the `if` structure.

The second error is a different one. You’re failing to add a channel to `sam_to_bam_ch` and then Nextflow complains that you said the subworkflow would emit `sam_to_bam_ch` but the channel doesn’t exist.

---

<div class="post-metadata">

**Author:** ![bskubi](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/bskubi/32/545_2.png) [@bskubi](https://community.seqera.io/u/bskubi)\
**Post date:** [March 21, 2024, 6:41pm UTC](https://community.seqera.io/t/variable-defined-w-def-gives-missing-name-with-which-to-set-the-channel-variable/582/3 "2024-03-21T18:41:48Z")

</div>

Thanks for those links, that’s helpful.

---

<div class="post-metadata">

**Author:** ![mribeirodantas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mribeirodantas/32/235_2.png) [@mribeirodantas](https://community.seqera.io/u/mribeirodantas)\
**Post date:** [March 22, 2024, 12:00am UTC](https://community.seqera.io/t/variable-defined-w-def-gives-missing-name-with-which-to-set-the-channel-variable/582/4 "2024-03-22T00:00:27Z")

</div>

Please, mark my answer as a solution if it solved your problem 😉