test-metapipeline-DNA-batch test case always reports success

[nwiltsie]

From /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/nwiltsie-weblog-tests/log-nftest-20240524T155147Z.log...

2024-05-24 15:59:20,593 - NextFlow - INFO -
2024-05-24 15:59:20,610 - NextFlow - INFO - executor >  local (2), slurm (1)
2024-05-24 15:59:20,611 - NextFlow - INFO - [10/7acd4f] process > create_CSV_metapipeline_DNA... [100%] 1 of 1 ✔
2024-05-24 15:59:20,612 - NextFlow - INFO - [75/64d2d6] process > create_config_metapipeline_... [100%] 1 of 1 ✔
2024-05-24 15:59:20,612 - NextFlow - INFO - [5b/cda13c] process > call_metapipeline_DNA (1)      [100%] 1 of 1, failed: 1 ✔
2024-05-24 15:59:20,612 - NextFlow - INFO - [-        ] process > check_process_status           -
2024-05-24 15:59:20,612 - NextFlow - INFO - [5b/cda13c] NOTE: Process `call_metapipeline_DNA (1)` terminated with an error exit status (143) -- Error is ignored
2024-05-24 15:59:20,612 - NextFlow - INFO - Completed at: 24-May-2024 08:59:20
2024-05-24 15:59:20,815 - NextFlow - INFO - Duration    : 7m 13s
2024-05-24 15:59:20,815 - NextFlow - INFO - CPU hours   : 1.1 (100% failed)
2024-05-24 15:59:20,815 - NextFlow - INFO - Succeeded   : 2
2024-05-24 15:59:20,815 - NextFlow - INFO - Ignored     : 1
2024-05-24 15:59:20,815 - NextFlow - INFO - Failed      : 1
2024-05-24 15:59:20,815 - NextFlow - INFO -
2024-05-24 15:59:20,815 - NextFlow - INFO -
2024-05-24 15:59:20,856 - NFTest - INFO -  [ succeed ]
2024-05-24 15:59:21,489 - NFTest - INFO - test-metapipeline-DNA-fastq-input: Test running the main.nf that runs the metapipeline-DNA pipeline in batch with fastq inputs.
2024-05-24 15:59:21,489 - NFTest - INFO -  [ skipped ]

I think the issue is that the check_process_status process does not bubble-up failures, so it will also always succeed. That particular NFTest case also has no file checks, so as long as the test gets to the point of the check_process_status loop it will always pass.

metapipeline-DNA/nftest.yaml

Lines 219 to 224 in e3c5367

	- name: test-metapipeline-DNA-batch
	message: Test running the main.nf that runs the metapipeline-DNA pipeline in batch.
	nf_script: main.nf
	nf_config: test/test-metapipeline-DNA-batch/test.config
	verbose: true
	skip: true

[yashpatel6]

Right, the test is set up to just run the case successfully and a failing process within Nextflow isn't propagated as the Nextflow command itself failing and so NFTest thinks it's a success. But it should be updated to add an actual status check