pin java version 21 in CI

sanger-tol · Dec 3, 2024 · 00b8ae0 · 00b8ae0
1 parent e9ed94e
commit 00b8ae0
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Showing 6 changed files with 6 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -26,6 +26,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  JAVA_HOME: $JAVA_HOME_21_X64
 
 jobs:
   download:
-Original file line number
+Diff line change
@@ Expand Up / @@ -26,6 +26,7 @@ on: @@
     env:
       NXF_ANSI_LOG: false
+      JAVA_HOME: $JAVA_HOME_21_X64
     jobs:
       download:
@@ Expand Down @@