update to checkout v4

.github/workflows/add_fastani_ref.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
         - name: Checkout
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
           with:
             lfs: true
 

.github/workflows/current.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/ecoli.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/just_msa.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/klebsiella.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/legionella.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/myco.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/phylogenetic_workflow.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/run_workflow.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/salmonella.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/sample_sheet.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/strepA.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/strep_pneumo.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: Test Grandeur workflow profile test0
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Checkout LFS objects
+        run: git lfs checkout
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+          
+      - name: Run Grandeur
+        run: |
+          nextflow run . -profile docker,test0 -c .github/workflows/github_actions.config
+      
+      - name: Check contig files
+        run: |
+          for file in grandeur/contigs/*_contigs.fa
+          do
+            head $file
+            wc -l $file
+          done      

.github/workflows/versions.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/vibrio.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true
 

.github/workflows/withoutfastani.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           lfs: true