Fail-nf

A mini (dumb) nextflow pipeline to test pipeline failures in general :D.

Usage

Running without parameters will run the pipeline to completion sucessfully:

nextflow run main.nf

Simulate failures

Intermitent failures

To simulate a process with intermitent failures (some process executions fail while others pass) that retry up to 3 times and them the error is ignored:

nextflow run main.nf --alwaysPassIntermitentProcess=false

You can override the default error strategy using a parameter as well:

nextflow run main.nf --alwaysPassIntermitentProcess=false \
  --intermitentProcessErrorStrategy="terminate"

Simulate failure of terminal (non-critical) process

To simulate the failure of a "secondary" non-critical process, which is ignored and does not prevent the rest of the pipeline to complete:

nextflow run main.nf --abortTerminalProcess

The default error strategy for this process can also be override:

nextflow run main.nf --abortTerminalProcess \
  --terminalProcessErrorStrategy="terminate"

Simulate critical process failure

To simulate the failure of a critical pipeline process that prevents downstream processes from being executed:

nextflow run main.nf --abortCriticalProcess

Simulate missing output file failure

To simulate the failure of processes due to missing declared output files:

nextflow run main.nf --forceMissingOutputFail

Change simulated run time

You can set different ranges of run times (in seconds) for three processes, which can be combined with any of the failure options above:

nextflow run main.nf --terminalProcessTimeRange="10-20" \
  --intermitentProcessTimeRange="1-1" \
  --missingOutputProcessTimeRange="100-120"