Merge pull request #1363 from ggabernet/fix-ci

Fix tools CI workflows
nf-core · Dec 14, 2021 · 8cca94c · 8cca94c
2 parents 7719f3c + cc54b9e
commit 8cca94c
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Showing 3 changed files with 33 additions and 12 deletions.
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -1,15 +1,25 @@
 name: Create a pipeline and lint it
 on: [push, pull_request]
 
+env:
+  NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
+
 jobs:
   MakeTestWorkflow:
     runs-on: ubuntu-latest
     env:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and latest edge version
-        nxf_ver: ["NXF_VER=21.10.3", "NXF_EDGE=1"]
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -26,12 +36,13 @@ jobs:
 
       - name: Install Nextflow
         env:
-          CAPSULE_LOG: none
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-          export ${{ matrix.nxf_ver }}
-          nextflow self-update
 
       - name: nf-core create
         run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -1,17 +1,25 @@
 name: Create a pipeline and test it
 on: [push, pull_request]
 
+env:
+  NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
+
 jobs:
   RunTestWorkflow:
     runs-on: ubuntu-latest
     env:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and latest edge version
-        nxf_ver: 
-          - "NXF_VER=21.10.3"
-          # - "NXF_EDGE=1"
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -28,12 +36,13 @@ jobs:
 
       - name: Install Nextflow
         env:
-          CAPSULE_LOG: none
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-          export ${{ matrix.nxf_ver }}
-          nextflow self-update
 
       - name: Run nf-core/tools
         run: |

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -40,6 +40,7 @@
 * Erase temporary files and folders while performing Python tests (pytest)
 * Remove base `Dockerfile` used for DSL1 pipeline container builds
 * Run tests with Python 3.10
+* [#1363](https://github.com/nf-core/tools/pull/1363) Fix tools CI workflow nextflow versions.
 
 ### Modules