From 00b8ae0da46a7562be763c9efa6b82c696a362ba Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 3 Dec 2024 14:18:06 +0100
Subject: [PATCH] pin java version 21 in CI

---
 .github/actions/create-lint-wf/action.yml                     | 1 -
 .github/workflows/create-lint-wf.yml                          | 4 +---
 .github/workflows/create-test-lint-wf-template.yml            | 2 ++
 .github/workflows/create-test-wf.yml                          | 4 +---
 nf_core/pipeline-template/.github/workflows/ci.yml            | 1 +
 .../pipeline-template/.github/workflows/download_pipeline.yml | 1 +
 6 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
index 3ef0760513..3ffd960d23 100644
--- a/.github/actions/create-lint-wf/action.yml
+++ b/.github/actions/create-lint-wf/action.yml
@@ -15,7 +15,6 @@ runs:
         cd create-lint-wf
         export NXF_WORK=$(pwd)
 
-    # Set up Nextflow
     - name: Install Nextflow
       uses: nf-core/setup-nextflow@v2
       with:
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 37ab71bc3b..78932871e3 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -27,14 +27,12 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-env:
-  NXF_ANSI_LOG: false
-
 jobs:
   MakeTestWorkflow:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
+      JAVA_HOME: $JAVA_HOME_21_X64
     strategy:
       matrix:
         NXF_VER:
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index fffa9ffe7a..b0d4c13a4e 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -28,6 +28,7 @@ concurrency:
 
 env:
   NXF_ANSI_LOG: false
+  JAVA_HOME: $JAVA_HOME_21_X64
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
@@ -51,6 +52,7 @@ jobs:
     needs: prepare-matrix
     env:
       NXF_ANSI_LOG: false
+      JAVA_HOME: $JAVA_HOME_21_X64
     strategy:
       matrix:
         TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 93581b9153..f69449dde3 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -27,15 +27,13 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-env:
-  NXF_ANSI_LOG: false
-
 jobs:
   RunTestWorkflow:
     # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
+      JAVA_HOME: $JAVA_HOME_21_X64
     strategy:
       matrix:
         NXF_VER:
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 9db393d9f0..4f005a1bb4 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -11,6 +11,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  JAVA_HOME: $JAVA_HOME_21_X64
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 05397358cf..95ebad9fe4 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -26,6 +26,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  JAVA_HOME: $JAVA_HOME_21_X64
 
 jobs:
   download: