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SEAB-7772 Bump nextflow-parsing to Java 21 and align with dockstore versions #203

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SEAB-7772 Bump nextflow-parsing to Java 21 and align with dockstore versions #203

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17bbf71
Bump nextflow-parsing to Java 21 and align versions with dockstore
denis-yuen Oct 8, 2026
411870c
Update CLAUDE.md: Java 21 for nextflow-parsing, review before push
denis-yuen Oct 8, 2026
aad08ae
Align nextflow-parsing with Dockstore: checkstyle, jakarta, Nextflow …
denis-yuen Oct 8, 2026
f15d5c2
Fix nextflow-parsing handler and invoke it in CI against a real event
denis-yuen Oct 8, 2026
780dd19
Load Dockstore checkstyle config from the pinned 1.20.0 release URL
denis-yuen Oct 8, 2026
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4 changes: 3 additions & 1 deletion .github/workflows/maven.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,13 @@ jobs:
sam build --use-container
sam local invoke WDLParsingFunction -e events/event.json &> output.txt
grep "statusCode\": 200" output.txt
- name: Test Nextflow parsing with SAM CLI build (no invoke)
- name: Test Nextflow parsing with SAM CLI build and invoke
working-directory: ./nextflow-parsing
# SAM build also runs the Java tests
run: |
sam build --use-container
sam local invoke HelloWorldFunction -e events/sarek.json &> output.txt

@denis-yuen denis-yuen Oct 9, 2026

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One of the real changes

grep "statusCode\": 200" output.txt
- name: Build CWL packing with SAM CLI build (no invoke, no test)
working-directory: ./cwlpack
run: sam build --use-container
Expand Down
7 changes: 5 additions & 2 deletions CLAUDE.md
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Expand Up @@ -11,7 +11,7 @@ A monorepo of small, independent AWS Lambda functions used by Dockstore ("backup
| `checkUrlExists/` | Node 22 (`lambda/index.js`) | Checks a URL (http/https/ftp/sftp) is reachable; always returns 200, body is true/false |
| `cwlpack/` | Python 3.12 (`cwl_pack_function/app.py`) | Clones a git repo with pygit2 and packs a CWL descriptor with sbpack |
| `wdl-parsing/` | Java 21 (`WDLParsingFunction`, Maven) | Parses WDL descriptors |
| `nextflow-parsing/` | Java 11 template (`NextflowParsingFunction`, Maven) | Parses Nextflow descriptors |
| `nextflow-parsing/` | Java 21 (`NextflowParsingFunction`, Maven) | Parses Nextflow descriptors |
| `cloud-watch-to-slack-testing/`, `upsertGitHubTag/` | Node (`deployment/index.js`) | Not SAM; zipped and uploaded to S3 by CircleCI. `upsertGitHubTag` relays API Gateway -> SQS -> Lambda -> Dockstore webservice |

## Commands
Expand Down Expand Up @@ -59,7 +59,10 @@ When creating a PR, always create it in draft mode. A human developer must be th
review/move it out of draft state — Claude Code should not do this itself.

Always check with the user before pushing changes to GitHub, even to a branch/PR already being worked on in
the conversation — a push can kick off a long CI build or interrupt one that's already running.
the conversation — a push can kick off a long CI build or interrupt one that's already running. Before asking,
show the user what would be pushed (e.g. `git log` and `git diff` against the remote branch) so they can review
it first. An earlier "push" request does not cover later commits, and a force-push (e.g. after a rebase)
always needs explicit approval.

When a GitHub MCP server or `gh` is available, diff the current work against `develop` (or whatever branch the
PR targets) and try to minimize stylistic or otherwise-minor changes that inflate the diff and make it harder
Expand Down
5 changes: 5 additions & 0 deletions nextflow-parsing/NextflowParsingFunction/ignore.xml
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Expand Up @@ -13,4 +13,9 @@
<Match>
<Source name="ApiClient.java"/>
</Match>
<!-- NextflowHandler is a simple bean; newer SpotBugs flags its getters/setters -->
<Match>
<Class name="io.dockstore.nextflowparsing.NextflowHandler"/>
<Bug pattern="EI_EXPOSE_REP,EI_EXPOSE_REP2"/>
</Match>
</FindBugsFilter>
63 changes: 38 additions & 25 deletions nextflow-parsing/NextflowParsingFunction/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@
<packaging>jar</packaging>
<name>Nextflow parser created for SAM CLI.</name>
<properties>
<maven-plugin-version>3.0.0-M5</maven-plugin-version>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<junit-version>5.7.2</junit-version>
<jersey-version>2.34</jersey-version>
<maven-plugin-version>3.5.3</maven-plugin-version>
<maven.compiler.source>21</maven.compiler.source>
<maven.compiler.target>21</maven.compiler.target>
<junit-version>5.9.1</junit-version>
<jersey-version>3.1.11</jersey-version>
<jackson-version>2.22.3</jackson-version>
</properties>
<repositories>
Expand Down Expand Up @@ -43,7 +43,7 @@
<dependency>
<groupId>org.eclipse.jgit</groupId>
<artifactId>org.eclipse.jgit</artifactId>
<version>5.13.4.202507202350-r</version>
<version>7.8.0.202609011348-r</version>
</dependency>

<!-- JSON processing: jackson -->
Expand All @@ -56,17 +56,17 @@
<dependency>
<groupId>jakarta.ws.rs</groupId>
<artifactId>jakarta.ws.rs-api</artifactId>
<version>2.1.6</version>
<version>3.1.0</version>
</dependency>
<dependency>
<artifactId>aws-lambda-java-core</artifactId>
<groupId>com.amazonaws</groupId>
<version>1.2.1</version>
<version>1.4.0</version>
</dependency>
<dependency>
<artifactId>aws-lambda-java-events</artifactId>
<groupId>com.amazonaws</groupId>
<version>3.6.0</version>
<version>3.16.1</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
Expand All @@ -83,28 +83,35 @@
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.31</version>
<version>2.0.18</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>32.0.0-jre</version>
<version>33.6.0-jre</version>
</dependency>
<dependency>
<groupId>org.codehaus.groovy</groupId>
<groupId>org.apache.groovy</groupId>
<artifactId>groovy</artifactId>
<version>3.0.8</version>
<version>4.0.26</version>
</dependency>
<dependency>
<groupId>io.dockstore</groupId>
<artifactId>openapi-java-client</artifactId>
<version>1.12.0</version>
<version>1.20.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.nextflow</groupId>
<artifactId>nextflow</artifactId>
<version>21.04.3</version>
<version>25.04.4</version>
<exclusions>
<!-- only hosted on Seqera's own Maven repo; not needed to parse nextflow.config -->
<exclusion>
<groupId>io.seqera</groupId>
<artifactId>lib-trace</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<build>
Expand Down Expand Up @@ -135,7 +142,7 @@
</execution>
</executions>
<groupId>org.apache.maven.plugins</groupId>
<version>3.2.0</version>
<version>3.6.1</version>
</plugin>
<plugin>
<artifactId>spotbugs-maven-plugin</artifactId>
Expand All @@ -150,13 +157,14 @@
</execution>
</executions>
<groupId>com.github.spotbugs</groupId>
<version>4.0.4</version>
<version>4.8.3.1</version>
</plugin>
<plugin>
<artifactId>maven-checkstyle-plugin</artifactId>
<configuration>
<!-- Develop's latest commit for this checkstyle file -->
<configLocation>https://raw.githubusercontent.com/dockstore/lambda/a6ae4d98592b0d057c495bdb7b40c54e062ff998/wdl-parsing/WDLParsingFunction/checkstyle.xml</configLocation>
<!-- Dockstore's checkstyle config, pinned to the 1.20.0 release of dockstore/dockstore -->
<configLocation>https://raw.githubusercontent.com/dockstore/dockstore/1.20.0/checkstyle.xml</configLocation>
<suppressionsLocation>https://raw.githubusercontent.com/dockstore/dockstore/1.20.0/checkstyle-suppressions.xml</suppressionsLocation>
<includeResources>true</includeResources>
<includeTestResources>true</includeTestResources>
<includeTestSourceDirectory>true</includeTestSourceDirectory>
Expand All @@ -165,7 +173,7 @@
<dependency>
<artifactId>checkstyle</artifactId>
<groupId>com.puppycrawl.tools</groupId>
<version>8.34</version>
<version>10.0</version>
</dependency>
</dependencies>
<executions>
Expand All @@ -182,15 +190,20 @@
</plugin>
<plugin>
<artifactId>fmt-maven-plugin</artifactId>
<configuration>
<!-- 4-space indentation to match the Dockstore checkstyle.xml -->
<style>aosp</style>
<skipSortingImports>true</skipSortingImports>
</configuration>
<executions>
<execution>
<goals>
<goal>format</goal>
</goals>
</execution>
</executions>
<groupId>com.coveo</groupId>
<version>2.10</version>
<groupId>com.spotify.fmt</groupId>
<version>2.29</version>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
Expand All @@ -210,10 +223,10 @@
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<groupId>org.apache.maven.plugins</groupId>
<version>3.8.1</version>
<version>3.12.1</version>
<configuration>
<source>11</source>
<target>11</target>
<source>21</source>
<target>21</target>
</configuration>
</plugin>
</plugins>
Expand Down
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