No project name was specified

[nick-youngblut]

Bug report

If one runs nextflow run with -with-report or -with-trace (and provides a "main" nextflow workflow file as input, such as main.nf), then one gets the error:

No project name was specified

There is no info in https://www.nextflow.io/docs/latest/tracing.html that I can find on how to set the project name. I have tried to set the project name via:

manifest {
  name = 'my_project_name'
}

...but that still results in the issue.

Expected behavior and actual behavior

Clear information on how to set the project name when using -with-report or -with-trace.

Steps to reproduce the problem

Nextflow version: 22.10.4.5836

Installed Nextflow via bioconda

Run

nextflow run  -profile aws,docker -with-trace -with-report main.nf 

Config

manifest {
  name = 'my_project_name'
}

profiles {
    docker {
        docker.enabled         = true
        docker.sudo            = true
        docker.runOptions      = '-u \$(id -u):\$(id -g)'
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    aws {
        process.executor   = 'awsbatch'
        process.queue      = 'my_process_queue'
    }
}

aws {
  batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
  accessKey = secrets.AWS_ACCESS_KEY_ID
  secretKey = secrets.AWS_SECRET_ACCESS_KEY
  region = secrets.AWS_DEFAULT_REGION
}

process {
    errorStrategy = 'retry'
    maxRetries    = 3
    maxErrors     = '-1'
}

Environment

• Nextflow version: 22.10.4.5836
• Java version: "17.0.3-internal" 2022-04-19
• Operating system: macOS
• Bash version: GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)

Maybe it would be useful to create a nextflow diagnose subcommand that lists all of these environment parameters?

[mribeirodantas]

Hm.. If you place the main.nf right after run it works, but when it's at the end it doesn't. Yeah, definitely looks like a bug!

[bentsherman]

Looks like the run command just expects the project name to be the first argument:

https://github.com/nextflow-io/nextflow/blob/41510e874644af8fe8986f04fa5bad20bb9a430f/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy#L279-L283

[maxulysse]

also, using -with-report main.nf means that you want the pipeline to create the report main.nf. cf https://www.nextflow.io/docs/latest/tracing.html#execution-report

[mribeirodantas]

Good point, @maxulysse !

[bentsherman]

I think this is the expected behavior. Not just with Nextflow but with CLIs in general -- positional args must always come before named args. However, I noticed the docs are incorrect: https://nextflow.io/docs/latest/cli.html#run

$ nextflow run [options] [project]

@mribeirodantas can you correct the docs here? I would also check the entire CLI docs page to see if this error was made for other commands. And the CLI output in Nextflow.

[mribeirodantas]

Sure! I saw the docs page yesterday and was wondering if this was really true. I will work on that.

[nick-youngblut]

It would help to clarify in the nextflow run docs which parameters are boolean versus which require a >=1 argument:

    -with-charliecloud
       Enable process execution in a Charliecloud container runtime
    -with-conda
       Use the specified Conda environment package or file (must end with
       .yml|.yaml suffix)
    -with-dag
       Create pipeline DAG file
    -with-docker
       Enable process execution in a Docker container
    -N, -with-notification
       Send a notification email on workflow completion to the specified
       recipients
    -with-podman
       Enable process execution in a Podman container
    -with-report
       Create processes execution html report
    -with-singularity
       Enable process execution in a Singularity container
    -with-timeline
       Create processes execution timeline file
    -with-tower
       Monitor workflow execution with Seqera Tower service
    -with-trace
       Create processes execution tracing file
    -with-weblog
       Send workflow status messages via HTTP to target URL
    -without-conda
       Disable the use of Conda environments
    -without-docker
       Disable process execution with Docker
       Default: false
    -without-podman
       Disable process execution in a Podman container
    -w, -work-dir
       Directory where intermediate result files are stored

[bentsherman]

I took another look here and it turns out I gave the wrong diagnosis. The problem is that some options like -with-report expect an argument but Nextflow will insert a default "-" if no argument is given. Unfortunately I don't think we can fix this with the current CLI.

We are working on a new CLI called nf (see #3595). I just tested it and I can do the following:

nf run --with-trace --with-report -- main.nf

The double dash allows you to separate positional arguments from optional arguments. But it doesn't seem to work with the current CLI. So I will tie this issue to the new CLI effort.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.