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I often find myself editing the workflow Makefiles when I'm investigating issues with spt workflow configure and nextflow run so I can see what's wrong with the processes being run by Nextflow and if the files being saved are correct.
I'd suggest that, when VERBOSE=1 during testing, the contents of the Nextflow work directories and logs are dumped to stdout before they're deleted.
The text was updated successfully, but these errors were encountered:
(Something else I do is delete test_proximity_pipeline.sh and test_umap_plot_creation.sh as well as add a dummy test test_a.sh when I just want to debug the cg-gnn workflow, so make module-test-workflow runs only the one script I need.)
You can run a single test using a direct call to make on the subdirectory with that Makefile. The tricky part is providing all the environment variables that are expected by the submake invocation.
The problem with dumping Nextflow logs by default is that they definitely overhwelm the logs in most normal cases with unimportant messages. I think a different verbose option should be implemented for this. When nextflow errors, it does dump relevant logs already by default, but this doesn't help you with monitoring normal runs.
I often find myself editing the
workflow
Makefiles when I'm investigating issues withspt workflow configure
andnextflow run
so I can see what's wrong with the processes being run by Nextflow and if the files being saved are correct.I'd suggest that, when
VERBOSE=1
during testing, the contents of the Nextflow work directories and logs are dumped to stdout before they're deleted.The text was updated successfully, but these errors were encountered: