docs: Add guide for bin scripts#933
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christopher-hakkaart merged 16 commits intomasterfrom Dec 14, 2025
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gwright99
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Left comments and thoughts. Good first pass but I feel that elaboration could be helpful for the average reader who doesn't yet have a full grasp on the inner workings of these various ecosystem components.
Tidying up PR - resolving agreed suggestions
…s/wave into docs-guide-bin-scripts
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Approving to get PR unblocked and on understanding discussed items will be handled in separate document at some future point.
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pditommaso
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Dec 11, 2025
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| When you enable Fusion or use the AWS Fargate executor, Wave bundles scripts from the project `bin/` directory into a container layer. This provides better performance but ties scripts to specific execution environments. Scripts are added to `/usr/local/bin/` in the container image, making them directly executable without path qualification. Remote `bin/` directory upload is disabled. | ||
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| Modifying scripts in the project `bin/` directory modify the container fingerprint for all Wave containers in the workflow. See [Wave container fingerprinting](#wave-container-fingerprinting) for more information. |
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This is a bit too technical, i'd focus it will result in creating a modified container, and therefore invalidating the cache for previous runs
pditommaso
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Dec 11, 2025
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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This PR adds documentation for Wave's
binscript bundling behavior in Nextflow pipelines. This guide helps users understand which scripts get packaged into container images and how this affects container fingerprinting and caching.This PR is intentionally limited in scope to address a specific user pain point: understanding how Wave handles bin scripts from different directories (
${projectDir}/bin/vs.${moduleDir}/resources/usr/bin/) and when those scripts are bundled into container layers.The guide covers:
binscripts are bundledI've tried to keep the scope limited and focus on the bin behavior without going too deep. Not covered here: