Fix cache invalidation for module binaries with Wave

[FloWuenne]

Summary

Fix task cache invalidation when using module binaries with Wave.

Task hashing previously considered project-level bin/ scripts but not module-level binaries under resources/usr/bin, which could cause stale cached tasks to be reused after a module binary changed.

This change makes task hashing resolve referenced executables from the task bin paths, including module binary directories, so module binary updates invalidate the cache as expected.

Closes #6128

Testing

• Added a regression test for module binary hash changes in TaskHasherTest
• Ran:
  • ./gradlew :nextflow:test --tests 'nextflow.processor.TaskHasherTest'

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[pditommaso]

Can you provide a reproducible test case for the problem are aiming to solve.

Module resources/bins are included via the container fingerprint, see here and here and here

[FloWuenne]

From the issue referenced #6128, someone wrote a minimal test pipeline: jashapiro/nextflow-resume-test.

We can test this fix using the following procedure:

git clone https://github.com/jashapiro/nextflow-resume-test.git
cd nextflow-resume-test

Run once:

nextflow run . -c inspect-wave.config -with-docker

where inspect-wave.config is:

wave.enabled = true
process.container = 'community.wave.seqera.io/library/samtools:1.21--0d76da7c3cf7751c'
nextflow.enable.moduleBinaries = true

Change the module binary and rerun with resume:

touch modules/test/resources/usr/bin/hello_test.sh
nextflow run . -c inspect-wave.config -with-docker -resume

Expected result with the fix:

Cached process > hello
Submitted process > test:test_hello

Before the fix, both processes could be restored from cache even after changing modules/test/resources/usr/bin/hello_test.sh.

The included groovy test in the PR should emulate the same behaviour. I have tested the fix using a local build of Nextflow with these changes and that worked.

@pditommaso Do you prefer the fix implementation via a different mechanism? If so, can you elaborate how?

[pditommaso]

If am i not wrong the test does not use wave https://github.com/jashapiro/nextflow-resume-test

[pditommaso]

Ok, managed to replicate:

• execution with wave: ok ✅
• execution without wave: module res changes are not detected ❌

[FloWuenne]

@pditommaso Thanks for replicating! Anything else missing to get this merged?

[pditommaso]

Yes, this PR requires merging this first #6927