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SEAB-7772 Bump nextflow-parsing to Java 21 and align with dockstore versions - #203
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denis-yuen
added this pull request to stack #201
October 8, 2026 20:22
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- Java 11 -> 21 (pom and template.yaml runtime java21) - Groovy 3.0.8 -> 3.0.25 (3.0.8 cannot read Java 21 class files) - fmt-maven-plugin -> com.spotify.fmt 2.29, dependency plugin 3.6.1, spotbugs 4.8.3.1, surefire/failsafe 3.5.3, compiler plugin 3.12.1 - jackson 2.22.1, guava 33.6.0-jre, slf4j-api 2.0.18, junit 5.9.1 - Ignore EI_EXPOSE_REP findings on NextflowHandler Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…25.04 - Use Dockstore's checkstyle.xml/suppressions (engine 10.0); format with fmt-maven-plugin aosp style (4-space) and unsorted imports to satisfy it - javax.ws.rs -> jakarta.ws.rs (jakarta.ws.rs-api 3.1.0, jersey 3.1.11, openapi-java-client 1.20.0) - jgit 5.12.0 -> 7.8.0 - Nextflow 21.04.3 -> 25.04.4 (ConfigParserFactory.create()), Groovy 4.0.26, excluding io.seqera:lib-trace (not on Maven Central, unused for parsing) - aws-lambda-java-core 1.4.0, aws-lambda-java-events 3.16.1 - Nextflow brings logback 1.5, fixing the slf4j 2.x no-op logging Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Replaces the local copies of checkstyle.xml and checkstyle-suppressions.xml (identical to dockstore/dockstore 1.20.0). Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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Looks like stack glitched on merge, need to fix it |
denis-yuen
marked this pull request as draft
October 9, 2026 17:29
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Oct 9, 2026
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Explicitly ignore whitespace when reviewing, this uses a newer checkstyle from dockstore
| # SAM build also runs the Java tests | ||
| run: | | ||
| sam build --use-container | ||
| sam local invoke HelloWorldFunction -e events/sarek.json &> output.txt |
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One of the real changes
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marked this pull request as ready for review
October 9, 2026 18:52
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Description
So things are easier to work with and explore, I updated all libraries for nextflow-parsing to more recent counterparts. I also had it flesh out the test so it actually invokes the nextflow lambda. FYI, not wedded to the git clone in the lambda, I may split it out to a different lambda or not even use it as discussed. This is mostly to get things working/easier to work with.
Generated comment:
Moves
nextflow-parsingto Java 21 and aligns it withdockstore/dockstore: Maven plugins, checkstyle (pinned 1.20.0 config),javax->jakarta, and library versions, including Nextflow 25.04.4 (Groovy 4, jgit 7). Fixes the template handler and invokes the function against a Sarek event in CI. Also updatesCLAUDE.md. Stacked on #202.Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-7772
Security
Changes the Lambda runtime (java11 -> java21) and many dependencies. Excludes Nextflow's
io.seqera:lib-traceinstead of adding a third-party Maven repo.Please make sure that you've checked the following before submitting your pull request. Thanks!
🤖 Generated with Claude Code