nextflow-io / nextflow-io/nextflow

Strict mode should also enforce existence of process labels

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error-improvements lang/config stale
Dominant language
Groovy
Stars
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Avg merge
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Merged PRs (30d)
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Description

New feature

Nextflow strict mode helps avoid a lot of troublesome silent errors, but it does not seem to throw an error if a process declares a label that does not exist in the config.

E.g. Adding a non-existent label to the classic Hello World script:

process sayHello {
  label 'doesnotexist'

  input: 
    val x
  output:
    stdout
  script:
    """
    echo '$x world!'
    """
}

workflow {
  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
}

But even with strict mode enabled, it runs without error:

$ NXF_ENABLE_STRICT=true nextflow run main.nf 
N E X T F L O W  ~  version 22.10.0
Launching `main.nf` [nostalgic_gates] DSL2 - revision: b366a11eb3
executor >  local (4)
[98/8ff160] process > sayHello (2) [100%] 4 of 4 ✔
Hello world!

Bonjour world!

Hola world!

Ciao world!

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the strict-mode behavior demonstrated by main.nf and run it with NXF_ENABLE_STRICT=true using nextflow run main.nf. Trace where the process label is checked, then make strict mode reject doesnotexist when it is absent from configuration; verify that the example no longer runs silently.

Written by the indexing model from the issue text.

Assessment

Tech stack
groovy
Domain
data-engineering
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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