emit breaks path output specifier inside tuple

[esrice]

Bug report

Expected behavior and actual behavior

A process output in DSL2 specified like this:

output:
    tuple(val(id), path("${id}.fa.fai")), emit: faidx

ought to work exactly the same as without the emit, with the exception that in the former case the output is named and in the latter it is not:

output:
    tuple(val(id), path("${id}.fa.fai"))

However, the version without emit works as expected, whereas the version with emit causes the following error:

Unknown process directive: `path`

Steps to reproduce the problem

Here is a simple DSL2 script I wrote to illustrate the issue:
pipeline.nf:

nextflow.enable.dsl = 2

process TEST {
    input:
        tuple(val(id), path("${id}.fa"))

    output:
        tuple(val(id), path("${id}.fa.fai")), emit: faidx

    """
    samtools faidx seq.fa
    """
}

workflow {
    Channel.fromPath("*.fa")
        .map { tuple (it.baseName, it) }
        .set { seqIn }

    TEST(seqIn)
}

Running nextflow run pipeline.nf crashes.

Program output

STDOUT:

N E X T F L O W  ~  version 22.10.6
Launching `pipeline.nf` [prickly_jones] DSL2 - revision: 9eeeab02b5
Unknown process directive: `path`

Did you mean of these?
        each

 -- Check script 'pipeline.nf' at line: 6 or see '.nextflow.log' file for more details

.nextflow.log:

Mar-10 07:26:34.455 [main] DEBUG nextflow.cli.Launcher - $> nextflow run pipeline.nf
Mar-10 07:26:34.545 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.10.6
Mar-10 07:26:34.566 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/esrbhb/.nextflow/plugins; core-plugins: [email protected],[email protected]
,[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Mar-10 07:26:34.579 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-10 07:26:34.581 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-10 07:26:34.584 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Mar-10 07:26:34.595 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Mar-10 07:26:34.651 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Mar-10 07:26:34.670 [main] INFO  nextflow.cli.CmdRun - Launching `pipeline.nf` [peaceful_jang] DSL2 - revision: 8427d1ae2f
Mar-10 07:26:34.671 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Mar-10 07:26:34.672 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Mar-10 07:26:34.683 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/esrbhb/.nextflow/secrets/store.json
Mar-10 07:26:34.690 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@585c13de] - activable => nextflow.secret.LocalSecretsProvider@585c13de
Mar-10 07:26:34.757 [main] DEBUG nextflow.Session - Session UUID: 490fed87-c6ad-4946-b925-727a0815c078
Mar-10 07:26:34.758 [main] DEBUG nextflow.Session - Run name: peaceful_jang
Mar-10 07:26:34.759 [main] DEBUG nextflow.Session - Executor pool size: 28
Mar-10 07:26:34.771 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=84; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Mar-10 07:26:34.810 [main] DEBUG nextflow.cli.CmdRun -
  Version: 22.10.6 build 5843
  Created: 23-01-2023 23:20 UTC (17:20 CDT)
  System: Linux 3.10.0-1127.10.1.el7.x86_64
  Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src
  Encoding: UTF-8 (UTF-8)
  Process: 27446@lewis4-r630-login-node676 [10.46.69.155]
  CPUs: 28 - Mem: 251.7 GB (4.9 GB) - Swap: 1024 MB (1024 MB)
Mar-10 07:26:34.844 [main] DEBUG nextflow.Session - Work-dir: /storage/hpc/group/warrenlab/users/esrbhb/nx_work [lustre]
Mar-10 07:26:34.846 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /storage/htc/warrenlab/users/esrbhb/nf_test/bin
Mar-10 07:26:34.865 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Mar-10 07:26:34.882 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-10 07:26:34.913 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Mar-10 07:26:34.927 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 29; maxThreads: 1000
Mar-10 07:26:35.015 [main] DEBUG nextflow.Session - Session start
Mar-10 07:26:35.829 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-10 07:26:35.972 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown process directive: `path`

Did you mean of these?
        each
Mar-10 07:26:35.992 [main] DEBUG nextflow.Session - The following nodes are still active:
  [operator] map

Mar-10 07:26:36.002 [main] ERROR nextflow.cli.Launcher - @unknown
nextflow.exception.IllegalDirectiveException: Unknown process directive: `path`

Environment

• Nextflow version: 22.10.6
• Java version: openjdk version "17.0.3-internal" 2022-04-19
• Operating system: CentOS Linux release 7.9.2009 (Core)
• Bash version: 4.2.46

[bentsherman]

When you use parentheses for the tuple, you have to put the emit inside the tuple:

output:
    tuple(val(id), path("${id}.fa.fai"), emit: faidx)

[esrice]

Thanks!