Improper error message returned with malformed outputs

[BeyondTheProof]

Bug report

Expected behavior and actual behavior

When outputting a malformed tuple (in this case, without commas separating), NF raises cryptic errors such as No such variable: sample and Process 'PRINT_INPUTS' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

Steps to reproduce the problem

print_inputs.nf:

nextflow.enable.dsl=2

process PRINT_INPUTS {
    input:
        tuple val(chrom), val(sample)
    output:
        tuple val(chrom), val(sample)

    script:
    """
    echo $chrom
    """
}

main.nf:

nextflow.enable.dsl = 2

include {PRINT_INPUTS} from './modules/print_inputs.nf'

workflow {
    chroms = Channel.from(1..3)
    samples = Channel.from("A", "B")
    input_channels = chroms.combine( samples )
    output = PRINT_INPUTS (input_channels)
}

Program output

...
Apr-04 22:51:12.576 [main] DEBUG nextflow.cli.CmdRun -
  Version: 23.01.0-edge build 5834
  Created: 14-01-2023 17:31 UTC
  System: Linux 5.15.0-1030-gcp
  Runtime: Groovy 3.0.14 on OpenJDK 64-Bit Server VM 17.0.6+10-Ubuntu-0ubuntu120.04.1
  Encoding: UTF-8 (UTF-8)
  Process: 129513@rome-repeat-genetics-jupyter-1 [10.128.0.3]
  CPUs: 16 - Mem: 102.2 GB (78.9 GB) - Swap: 0 (0)
Apr-04 22:51:12.642 [main] DEBUG nextflow.Session - Work-dir: /home/jupyter/work [ext2/ext3]
Apr-04 22:51:12.643 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/jupyter/project/new-targets/twas/nf_pipeline/bin
Apr-04 22:51:12.663 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Apr-04 22:51:12.686 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Apr-04 22:51:12.761 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Apr-04 22:51:12.780 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Apr-04 22:51:12.881 [main] DEBUG nextflow.Session - Session start
Apr-04 22:51:13.289 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Apr-04 22:51:13.763 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown variable 'sample'
Apr-04 22:51:13.794 [main] DEBUG nextflow.Session - The following nodes are still active:
  [operator] combine

Apr-04 22:51:13.806 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: Unknown variable 'sample'
...

Environment

• Nextflow version: 23.01.0-edge build 5834
• Java version: openjdk version "17.0.6" 2023-01-17
• Operating system: Linux
• Bash version: GNU bash, version 5.0.17(1)-release (x86_64-pc-linux-gnu)

Additional context

In the test case, I was unable to reproduce the original error I was getting -- Process 'PRINT_INPUTS' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context. I ran into that error in my own work, which I can't share, but it was caused by a missing comma between outputs in a tuple

[adamrtalbot]

Slack thread: https://nextflow.slack.com/archives/C02T98A23U7/p1686842054188879

Thanks to Clare Pacini and Alexander Nater for finding this issue. I was able to reproduce this like so:

Steps to reproduce the problem

sneakyerror.nf:

process SNEAKYERROR {

    input:
        tuple val(x) val(y)

    output:
        val z

    exec:
    z = x + y
}

workflow {
    ch_x = Channel.of("x")
    ch_y = Channel.of("y")

    SNEAKYERROR(ch_x, ch_y)
}

nextflow run sneakyerror.nf

Program output

N E X T F L O W  ~  version 23.04.1
Launching `sneakyerror.nf` [wise_cray] DSL2 - revision: 58faa1f628
Process 'SNEAKYERROR' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

 -- Check script 'misleading_error.nf' at line: 17 or see '.nextflow.log' file for more details

Environment

• Nextflow version: 23.04.1
• Java version: 17.0.7
• Operating system: Ubuntu 20.04.2 LTS
• Bash version: zsh 5.9 (x86_64-pc-linux-gnu)

[bentsherman]

Fixed by #4085