two input variables with identical names are allowed

[jgbaum]

Bug report

Nextflow seems to allow multiple input variables with identical names in the same process, which could lead to unexpected behavior.

Expected behavior and actual behavior

Nextflow should throw an error if a process contains multiple input variables with the same name.

Steps to reproduce the problem

Run the workflow below, which contains two input variables with the name 'sample_id'. This was originally taken from example 6.3.5 of the training documentation.

reads_ch = Channel.fromFilePairs('data/ggal/*_{1,2}.fq')

process FOO {
    input:
    tuple val(sample_id), path(sample_id)

    output:
    tuple val(sample_id), path('sample.bam')

    script:
    """
    echo your_command_here --reads $sample_id > sample.bam
    """
}

workflow {
    bam_ch = FOO(reads_ch)
    bam_ch.view()
}

Program output

N E X T F L O W  ~  version 22.10.7
Launching `processes.nf` [insane_goldstine] DSL2 - revision: 11430b8ce3
executor >  local (3)
[25/dbc431] process > FOO (2) [100%] 3 of 3 ✔
[[lung_1.fq, lung_2.fq], /Users/jgbaum/odrive/GDrive_LJI/_current_work/nextflow-training/random-scripts/work/b2/d2f9a3991d8f08d840546d2d80469c/sample.bam]
[[liver_1.fq, liver_2.fq], /Users/jgbaum/odrive/GDrive_LJI/_current_work/nextflow-training/random-scripts/work/c6/4905e0a1adf807ff156fc0dfff6d16/sample.bam]
[[gut_1.fq, gut_2.fq], /Users/jgbaum/odrive/GDrive_LJI/_current_work/nextflow-training/random-scripts/work/25/dbc4314edaca84665b1a89d57f4caa/sample.bam]

Environment

• Nextflow version: 22.10.7
• Java version: 17.0.6
• Operating system: macOS 13.3.1
• Bash version: zsh 5.9 (x86_64-apple-darwin22.0)

Additional context

This was originally raised in the nextflow training repo: https://github.com/nextflow-io/training/issues/231

[adrajago]

can I take this issue?

[bentsherman]

I think I made a PR for this already: #4376

Think it got stalled over concern that it would break existing pipelines, but seems like something that should break your pipeline

Maybe we could be more lenient and have it log a warning instead

[adrajago]

so have it send a warning to the user when inputting information?