docs: add Fusion symlink compaction troubleshooting#1195
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docs: add Fusion symlink compaction troubleshooting#1195
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…ractions Document Fusion's symlink compaction behavior — where output glob patterns from Nextflow's .command.run can cause input symlinks to be materialized as full copies at task shutdown. Includes diagnostic steps and guidance on narrowing output declarations to avoid unintended file copies. Signed-off-by: Rob Syme <rob.syme@gmail.com>
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Summary
fusion_docs/troubleshooting/nextflow.md) documenting Fusion's symlink compaction behavior when used with NextflowContext
Customers have encountered unexpected large file copies in task work directories when using Fusion with Nextflow. This happens when Nextflow output glob patterns inadvertently match input files staged as symlinks — Fusion's symlink compaction materializes these symlinks as full copies at task shutdown.
This behavior was previously undocumented. The new page covers:
output:declarations via.command.run.command.run(theoutputs:block andnxf_stage()symlinks)