Missing error detection when a tool does not exist

[ATpoint]

In this example below Nextflow will complete successfully despite the fact that there is a command which does not exist/is not in PATH:

#! /usr/bin/env nextflow

nextflow.enable.dsl=2

process A {

    output:
    path("foo.txt")

    script:
    """
    cmd1='echo 123'
    cmd2='echo 456'
    
    command_that_is_not_in_path <(eval \$cmd1) <(eval \$cmd2) \
    | head \
    | tail > foo.txt
    """

}

workflow { A() }

$ NXV_VER=21.10.6 nextflow run main.nf 
N E X T F L O W  ~  version 21.10.6
Launching `main.nf` [curious_avogadro] - revision: d2c8c9926f
executor >  local (1)
[d8/1b1296] process > A [100%] 1 of 1 ✔

BUT:

$ cat work/d8/1b1296184d04802a4b27425a57f6c1/.command.log 
/Users/atpoint/Desktop/work/d8/1b1296184d04802a4b27425a57f6c1/.command.sh: line 5: command_that_is_not_in_path: command not found

[pditommaso]

This is how Bash work. Start your script with:

set -o pipefail

to make it fail.