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[feature] Test dependencies automatically

Open adamrtalbot opened this issue 1 year ago • 1 comments

If a workflow uses a process, when that process is tested we could automatically include the subworkflow as a test. This can currently be achieved with tags (see #178) but it could be automatic.

This might fall out of what nf-test should be doing and instead be the responsibility of the pipeline developer. It may also relate to Nextflow dependencies which is a bigger issue. Worth discussion but possibly too far.

As an extension to #178 the process/workflow tag can be added to every workflow if it includes an include statement` which would solve this and provide some additional granularity.

Expected behaviour:

Where there is a samtools_sort process with a test in modules/processes/samtools_sort/, which is used in the workflow sort_and_view_with_samtools in modules/workflows/sort_view/:

nf-test test --tag samtools_sort

In addition to the expected samtools_sort test, automatically triggers the test for workflow sort_and_view_with_samtools. i.e., it is following the dependency.

adamrtalbot avatar Jan 22 '24 12:01 adamrtalbot