Add devcontainer (#6791)

[PeterKneale]

After opening the devcontainer in vscode, we can see the below versions are installed, and that compilation and tests are successful:

Versions

• java

vscode ➜ /workspaces/nextflow (Issue_6791) $ java --version
openjdk 24.0.2 2025-07-15
OpenJDK Runtime Environment Temurin-24.0.2+12 (build 24.0.2+12)
OpenJDK 64-Bit Server VM Temurin-24.0.2+12 (build 24.0.2+12, mixed mode, sharing)

• gradle

vscode ➜ /workspaces/nextflow (Issue_6791) $ gradle --version

------------------------------------------------------------
Gradle 9.2.0
------------------------------------------------------------

Build time:    2025-10-29 13:53:23 UTC
Revision:      d9d6bbce03b3d88c67ef5a0ff31f7ae5e332d6bf

Kotlin:        2.2.20
Groovy:        4.0.28
Ant:           Apache Ant(TM) version 1.10.15 compiled on August 25 2024
Launcher JVM:  24.0.2 (Eclipse Adoptium 24.0.2+12)
Daemon JVM:    /usr/local/sdkman/candidates/java/24.0.2-tem (no JDK specified, using current Java home)
OS:            Linux 6.17.8-orbstack-00308-g8f9c941121b1 aarch64

• groovy

vscode ➜ /workspaces/nextflow (Issue_6791) $ groovy --version
Groovy Version: 4.0.29 JVM: 24.0.2 Vendor: Eclipse Adoptium OS: Linux

Compilation

scode ➜ /workspaces/nextflow (Issue_6791) $ make
./gradlew compile exportClasspath

[Incubating] Problems report is available at: file:///workspaces/nextflow/build/reports/problems/problems-report.html

Deprecated Gradle features were used in this build, making it incompatible with Gradle 10.

You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.

For more on this, please refer to https://docs.gradle.org/9.2.0/userguide/command_line_interface.html#sec:command_line_warnings in the Gradle documentation.

BUILD SUCCESSFUL in 564ms
56 actionable tasks: 56 up-to-date
DONE Tue 03 Feb 2026 12:10:05 AM UTC

Launch

vscode ➜ /workspaces/nextflow (Issue_6791) $ ./launch.sh 
Usage: nextflow [options] COMMAND [arg...]

Options:
  -C
     Use the specified configuration file(s) overriding any defaults
*** SNIP***

Tests

vscode ➜ /workspaces/nextflow (Issue_6791) $ make smoke
NXF_SMOKE=1 ./gradlew test

> Task :nf-lang:compileJava
Note: /workspaces/nextflow/modules/nf-lang/src/main/java/nextflow/script/control/OpCriteriaVisitor.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

> Task :nextflow:compileGroovy
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

> Task :plugins:nf-amazon:compileGroovy
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: /workspaces/nextflow/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

> Task :plugins:nf-azure:compileGroovy
00:56:38.428 [/127.0.0.1:44030 to /127.0.0.1:39463 workers] DEBUG com.azure.core.implementation.ReflectionUtils -- Attempting to use java.lang.invoke package to handle reflection.
00:56:38.441 [/127.0.0.1:44030 to /127.0.0.1:39463 workers] DEBUG com.azure.core.implementation.ReflectionUtils -- Successfully used java.lang.invoke package to handle reflection.
00:56:52.598 [Test worker] DEBUG java.lang.Runtime -- Runtime.exit() called with status: 0
java.lang.Throwable: Runtime.exit(0)
        at java.base/java.lang.Shutdown.logRuntimeExit(Shutdown.java:179)
        at java.base/java.lang.Shutdown.exit(Shutdown.java:160)
        at java.base/java.lang.Runtime.exit(Runtime.java:188)
        at java.base/java.lang.System.exit(System.java:1920)
        at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:75)
00:58:26.391 [ForkJoinPool-1-worker-1] DEBUG o.e.jgit.internal.util.ShutdownHook – Cleanup org.eclipse.jgit.util.FS$FileStoreAttributes$$Lambda/0x000000a801f07ad0@544df82e during JVM shutdown

[Incubating] Problems report is available at: file:///workspaces/nextflow/build/reports/problems/problems-report.html

Deprecated Gradle features were used in this build, making it incompatible with Gradle 10.

You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.

For more on this, please refer to https://docs.gradle.org/9.2.0/userguide/command_line_interface.html#sec:command_line_warnings in the Gradle documentation.

BUILD SUCCESSFUL in 2m 22s
138 actionable tasks: 110 executed, 28 up-to-date
vscode ➜ /workspaces/nextflow (Issue_6791) $ 

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[PeterKneale]

@bentsherman
I've taken the dependency versions from the existing project and used them in the devcontainer.
They install cleanly and the project's make file produced a successful build on first attempt and the tests pass. Definately makes for an easier onboarding for new contributors.

[PeterKneale]

Any chance you can take a quick look at this @bentsherman , it works well for me and I used the environment to resolve another issue.

[PeterKnealeCMRI]

I dont suppose you could review this @ewels?

[ewels]

I think we can clean up most of these comments to keep this tidier. But otherwise it seems like a simple PR and a net-gain 👍🏻

[PeterKneale]

Fair enough! - comments removed. I had left them in case people were new to devcontainers but all good.