process directive not always applying to run

[anoronh4]

Bug report

Under certain circumstances, with the newest version of nextflow (22.04.5), my process directives for errorStrategy and maxRetries are being ignored.

process.errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
process.maxRetries = 3

is set from a config profile (using includeConfig statements), and the log says it has loaded the profile.

Expected behavior and actual behavior

Based on the directives we expect a failing process to retry or ignore. However the first process to encounter an error terminates without retrying, and kills the nextflow run, so it doesn't ignore either. Strangely, pipeline works as expected with older versions such 21.10.6.

Also a bit strange, if i move the process.* directives above into a process closure as such:

process {
...
errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
maxRetries = 3
} 
// process.errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
// process.maxRetries = 3

then it will work. Also, if i reorder my includeConfig commands the main nextflow config, i can also get the error to go away. So I can work around the problem but it still seems to me that there is an issue.

Steps to reproduce the problem

I found this while working on a bigger project that is not publicly available but i have reproduced it here:
https://github.com/anoronh4/nextflow_config_bug

Program output

N E X T F L O W  ~  version 22.04.5
Launching `test.nf` [prickly_panini] DSL2 - revision: efce412888
executor >  local (5)
executor >  local (5)
[a5/0ea02b] process > built2Fail (3) [100%] 5 of 5, failed: 1 ✘
WARN: There's no process matching config selector: SampleRunMultiQC
WARN: There's no process matching config selector: AggregateRunMultiQC
Error executing process > 'built2Fail (1)'

Caused by:
  Process `built2Fail (1)` terminated with an error exit status (1)

Command executed:

  echo "TERMINATE"
  if [ "DUP" == "DUP" ] ; then exit 1 ;fi

Command exit status:
  1

Command output:
  TERMINATE

Command wrapper:
  nxf-scratch-dir myserver:/scratch/anoronh4/nxf.U7VknhKC3E
  TERMINATE

Work dir:
  /path/to/mydir/bug_report/work/8e/62341efe0eb72c7b513bc36041167f

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Environment

• Nextflow version: 22.04.5
• Java version: 11
• Operating system: Linux
• Bash version: GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)

[bentsherman]

I think it's the same as #2966 , sometimes config options with the dot notation can be ignored if the block notation is also used. For now put everything in a block (closure) to be safe. We intend to address this problem by overhauling the config syntax (#2723).

[stale]

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.