diff --git a/.github/workflows/add_fastani_ref.yml b/.github/workflows/add_fastani_ref.yml index 2ae00e2..6cbb997 100755 --- a/.github/workflows/add_fastani_ref.yml +++ b/.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 diff --git a/.github/workflows/current.yml b/.github/workflows/current.yml index 9bf34a2..97c3e03 100644 --- a/.github/workflows/current.yml +++ b/.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 diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml index 7284f7c..c230174 100644 --- a/.github/workflows/ecoli.yml +++ b/.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 diff --git a/.github/workflows/just_msa.yml b/.github/workflows/just_msa.yml index dbbaa16..02eed2e 100644 --- a/.github/workflows/just_msa.yml +++ b/.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 diff --git a/.github/workflows/klebsiella.yml b/.github/workflows/klebsiella.yml index 69d6a3d..d3e8350 100755 --- a/.github/workflows/klebsiella.yml +++ b/.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 diff --git a/.github/workflows/legionella.yml b/.github/workflows/legionella.yml index 75ed8b8..78a2fd0 100644 --- a/.github/workflows/legionella.yml +++ b/.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 diff --git a/.github/workflows/myco.yml b/.github/workflows/myco.yml index fff6dec..cfe7d9c 100755 --- a/.github/workflows/myco.yml +++ b/.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 diff --git a/.github/workflows/phylogenetic_workflow.yml b/.github/workflows/phylogenetic_workflow.yml index 6027dd6..3dba0bc 100644 --- a/.github/workflows/phylogenetic_workflow.yml +++ b/.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 diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml index 59da4a0..99901c4 100644 --- a/.github/workflows/run_workflow.yml +++ b/.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 diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml index b51ccaa..f01563b 100644 --- a/.github/workflows/salmonella.yml +++ b/.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 diff --git a/.github/workflows/sample_sheet.yml b/.github/workflows/sample_sheet.yml index effdf8a..36fb418 100755 --- a/.github/workflows/sample_sheet.yml +++ b/.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 diff --git a/.github/workflows/strepA.yml b/.github/workflows/strepA.yml index 1719473..9caf9b5 100644 --- a/.github/workflows/strepA.yml +++ b/.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 diff --git a/.github/workflows/strep_pneumo.yml b/.github/workflows/strep_pneumo.yml index f503a17..df03a05 100644 --- a/.github/workflows/strep_pneumo.yml +++ b/.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 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100755 index 0000000..6384516 --- /dev/null +++ b/.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 diff --git a/.github/workflows/versions.yml b/.github/workflows/versions.yml index 5268412..38eaea2 100644 --- a/.github/workflows/versions.yml +++ b/.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 diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml index 7eacddb..219f6a0 100644 --- a/.github/workflows/vibrio.yml +++ b/.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 diff --git a/.github/workflows/withoutfastani.yml b/.github/workflows/withoutfastani.yml index 6461feb..a4374ba 100644 --- a/.github/workflows/withoutfastani.yml +++ b/.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