nfcoreLibraryLinker: exit gracefully when directories don't exist#50
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maxulysse
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Oct 6, 2025
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Presently, the nfcoreLibraryLinker function throws an exception if either the temporary nf-core library or the target modules directory do not exist.
This causes some issues with tests that call this function in the
cleanup {}block of an nf-test, when nf-test is executed in--dry-runmode, as the dry-run mode tries to execute the cleanup block (but not the setup block): askimed/nf-test#330See e.g. https://github.com/sanger-tol/nf-core-modules/blob/main/modules/sanger-tol/hiccramalign/minimap2align/tests/main.nf.test for an example of a test that fails.
This PR modifies the nfcoreLibraryLinker function to print a warning and exit gracefully when either directory doesn't exist (because set-up hasn't run). This is safe because if the directories don't exist, nothing should have been linked to or from them in any case.
This will temporarily side-step the problem we are having until it can be fixed upstream in nf-test.