added nextflow -version

UPHL-BioNGS · Feb 23, 2024 · 175a4fe · 175a4fe
1 parent 3d4c000
commit 175a4fe
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Showing 17 changed files with 41 additions and 90 deletions.
diff --git a/.github/workflows/add_fastani_ref.yml b/.github/workflows/add_fastani_ref.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+            nextflow -version
           
         - name: Download fastas
           run: |

diff --git a/.github/workflows/current.yml b/.github/workflows/current.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/just_msa.yml b/.github/workflows/just_msa.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/klebsiella.yml b/.github/workflows/klebsiella.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/legionella.yml b/.github/workflows/legionella.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/myco.yml b/.github/workflows/myco.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/phylogenetic_workflow.yml b/.github/workflows/phylogenetic_workflow.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |
@@ -33,12 +30,10 @@ jobs:
           mkdir fastas
           mv *fna fastas/.
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker,msa -c .github/workflows/github_actions.config --fastas fastas
 
           cat grandeur/grandeur_summary.tsv
 
-          nextflow run . -profile docker,msa -resume -c .github/workflows/github_actions.config --fastas fastas
-
       - name: Check MSA files
         run: |
           for file in grandeur/*/summary_statistics.txt grandeur/iqtree2/iqtree.treefile.nwk grandeur/snp-dists/snp_matrix.txt

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/sample_sheet.yml b/.github/workflows/sample_sheet.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/strepA.yml b/.github/workflows/strepA.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/strep_pneumo.yml b/.github/workflows/strep_pneumo.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/versions.yml b/.github/workflows/versions.yml
@@ -11,11 +11,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          lfs: true
-
-      - name: Checkout LFS objects
-        run: git lfs checkout
 
       - name: versions
         run: |

diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |

diff --git a/.github/workflows/withoutfastani.yml b/.github/workflows/withoutfastani.yml
@@ -9,16 +9,13 @@ jobs:
     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/
+
+          nextflow -version
           
       - name: Run Grandeur
         run: |
@@ -33,8 +30,14 @@ jobs:
           mkdir fastas
           mv *fna fastas/.
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
+          nextflow run . -profile docker,msa -c .github/workflows/github_actions.config --fastas fastas --exclude_top_hit
 
           cat grandeur/grandeur_summary.tsv
 
-          nextflow run . -profile docker,msa -resume --exclude_top_hit
+      - name: Check MSA files
+        run: |
+          for file in grandeur/*/summary_statistics.txt grandeur/iqtree2/iqtree.treefile.nwk grandeur/snp-dists/snp_matrix.txt
+          do
+            head $file
+            wc -l $file
+          done