From 4ebae21a419c4e442e7a37db193e033408f0ef41 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Wed, 4 Dec 2024 10:30:35 +0100
Subject: [PATCH] FIX: add setup java 17 (#1743)

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## PR checklist

- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add
tests!
- [ ] If you've added a new tool - have you followed the pipeline
conventions in the [contribution
docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/nf-core/test-datasets)
repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker
--outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run .
-profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and
authors/contributors).
---
 .github/workflows/ci.yml     | 5 +++++
 .github/workflows/pytest.yml | 5 +++++
 CHANGELOG.md                 | 1 +
 3 files changed, 11 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8ed6cebe7e..1de1e12694 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -57,6 +57,11 @@ jobs:
           python-version: "3.11"
           architecture: "x64"
 
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 978db90c48..bd1dcae14c 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -87,6 +87,11 @@ jobs:
       - name: Install Python dependencies
         run: pip install --upgrade -r tests/requirements.txt
 
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
       - name: Install Nextflow ${{ matrix.NXF_VER }}
         uses: nf-core/setup-nextflow@v2
         with:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1d8c61f939..0876f35e9d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json
 - [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode
 - [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet
+- [1743](https://github.com/nf-core/sarek/pull/1743) - Add setup java 17 in GHA for latest Nextflow version
 
 ### Removed