Typo in the container declaration leads to null and nextflow using a local tool installation

[FriederikeHanssen]

Bug report

When the container definition ends on [], the container itself is not used but the container declaration is set to null. If the tool is available locally, nextflow uses that tool and the script is not portable anymore.

Expected behavior and actual behavior

Such a typo should throw an error and warn the user

Steps to reproduce the problem

I created a small example here: https://github.com/FriederikeHanssen/mre/blob/container_typo/main.nf

The container declaration ends on []. If cowsay is not installed in my local environment the script fails with .command.sh: line 2: cowpy: command not found. However, if I have it installed in my local environment (i.e pip install cowpy ) The script finishes successfully.

Program output

The .command.run:

#!/bin/bash
### ---
### name: 'COWSAY'
### container: 'null'
### ...
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}

Environment

• Nextflow version: 24.10.3.5933
• Operating system: macOS

[pditommaso]

Emm, why there's a [] after the container name! 😆

[FriederikeHanssen]

Typos happen

[pditommaso]

Not sure how much it can be done, it's valid syntax returning an empty string

def x = 'foo'[]
assert x == ''

[bentsherman]

This syntax is not valid with the language server / new script parser. Will be fixed by #4613