Don't use System.exit(1)

[ewels]

We've been giving @pditommaso nightmares with our use of System.exit:

tools/nf_core/pipeline-template/lib/WorkflowPipeline.groovy

Lines 16 to 17 in bc56cdd

	log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
	System.exit(1)

$ nextflow run .
N E X T F L O W  ~  version 22.08.2-edge
Launching `./main.nf` [crazy_swirles] DSL2 - revision: 6b60f60cc2
Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.

Instead, we should be using exceptions:

throw new Exception("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.")

$ nextflow run .
N E X T F L O W  ~  version 22.08.2-edge
Launching `./main.nf` [cranky_roentgen] DSL2 - revision: 62f715c40c
Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.

 -- Check script 'main.nf' at line: 1 or see '.nextflow.log' file for more details

TODO

• Remove from the template
• Add lint tests that search all files for System.exit

[ewels]

An easier method is to use error which is a wrapper around calling an exception.

error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.")

[awgymer]

Cannot push my code right now due to some GitHub issue but I had a go at writing some lint code:

╭─ [!] 6 Pipeline Test Warnings 
│ system_exit: System.exit in WorkflowNanoporeqc.groovy: System.exit(1)                                                                                                                            
│ system_exit: System.exit in WorkflowNanoporeqc.groovy: System.exit(1)                                                                                                                            
│ system_exit: System.exit in NfcoreSchema.groovy: System.exit(1)                                                                                                                                  
│ system_exit: System.exit in WorkflowMain.groovy: System.exit(0)                                                                                                                                  
│ system_exit: System.exit in WorkflowMain.groovy: System.exit(0)                                                                                                                                  
│ system_exit: System.exit in WorkflowMain.groovy: System.exit(1)                                                                                                                                  

So I think this should inform the template changes to make too.

[drpatelh]

See commit for how we should replace System.exit(1) calls in the pipeline template with Nextflow.error(message). Will need to update the Schema validation script too.

At the moment Nextflow still generates the -- Check script message which we don't really want because it could cause confusion with users because the failure is expected:

* Software dependencies
  https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
------------------------------------------------------
Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.

 -- Check script './workflows/rnaseq.nf' at line: 17 or see '.nextflow.log' file for more details

I asked Paolo to fix this just now and it's done so will be available in the next NF release:
nextflow-io/nextflow@38c8bd3

[awgymer]

Closed in #2211