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Add -project-dir option to lint command#6728

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bentsherman merged 2 commits intomasterfrom
cmd-lint-lib-dir
Mar 19, 2026
Merged

Add -project-dir option to lint command#6728
bentsherman merged 2 commits intomasterfrom
cmd-lint-lib-dir

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@bentsherman bentsherman commented Jan 16, 2026 •
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Close #6634

This PR updates the nextflow lint command to recognize project-level assets such as the lib directory and modules directory

  • Add -project-dir option to nextflow lint (defaults to .)
  • Pass project dir to ScriptParser so that it can resolve remote module includes against modules directory
  • Move shared class loader logic to ClassLoaderFactory so that it can be used by both Session and CmdLint
  • Update ResolveVisitor to handle Groovy classes from the lib directory
  • Add unit test based on linked issue

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netlify Bot commented Jan 16, 2026 •
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✅ Deploy Preview for nextflow-docs-staging canceled.

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🔨 Latest commit cb14077
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@bentsherman bentsherman added this to the 26.04 milestone Feb 6, 2026
@pditommaso pditommaso force-pushed the master branch 2 times, most recently from d9fa5cd to d752bc2 Compare February 28, 2026 13:10
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bentsherman commented Mar 16, 2026

TODO: specify -project-dir instead of -lib-dir so that nextflow lint can understand any project-level entities -- lib dir, modules dir, etc

@bentsherman bentsherman changed the title Add -lib option to nextflow lint Add -project-dir option to lint command Mar 18, 2026
@bentsherman bentsherman marked this pull request as ready for review March 18, 2026 14:50
@bentsherman bentsherman requested review from a team as code owners March 18, 2026 14:50
@bentsherman bentsherman requested a review from jorgee March 18, 2026 14:56
@bentsherman
Add -project-dir option to lint command
ea4834f 
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
jorgee
jorgee reviewed Mar 19, 2026
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Comment thread modules/nf-lang/src/main/java/nextflow/script/control/GroovyCompiler.java Outdated
jorgee
jorgee reviewed Mar 19, 2026
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Comment thread modules/nf-lang/src/main/java/nextflow/script/control/ResolveVisitor.java
@bentsherman
Remove unnecessary try-catch
cb14077 
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
@bentsherman bentsherman requested a review from jorgee March 19, 2026 18:28
@bentsherman bentsherman merged commit 1679b9f into master Mar 19, 2026
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@bentsherman bentsherman deleted the cmd-lint-lib-dir branch March 19, 2026 19:33
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Successfully merging this pull request may close these issues.

Nextflow linter errors on custom Groovy code in lib/ as not being defined

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