From 175a4fe837abb9050664456e90e54dfe56b8f6c1 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Fri, 23 Feb 2024 10:11:28 -0700 Subject: [PATCH] added nextflow -version --- .github/workflows/add_fastani_ref.yml | 7 ++----- .github/workflows/current.yml | 7 ++----- .github/workflows/ecoli.yml | 7 ++----- .github/workflows/just_msa.yml | 7 ++----- .github/workflows/klebsiella.yml | 7 ++----- .github/workflows/legionella.yml | 7 ++----- .github/workflows/myco.yml | 7 ++----- .github/workflows/phylogenetic_workflow.yml | 11 +++-------- .github/workflows/run_workflow.yml | 7 ++----- .github/workflows/salmonella.yml | 7 ++----- .github/workflows/sample_sheet.yml | 7 ++----- .github/workflows/strepA.yml | 7 ++----- .github/workflows/strep_pneumo.yml | 7 ++----- .github/workflows/test.yml | 7 ++----- .github/workflows/versions.yml | 5 ----- .github/workflows/vibrio.yml | 7 ++----- .github/workflows/withoutfastani.yml | 17 ++++++++++------- 17 files changed, 41 insertions(+), 90 deletions(-) diff --git a/.github/workflows/add_fastani_ref.yml b/.github/workflows/add_fastani_ref.yml index 6cbb997..c0bcd8e 100755 --- 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 index 97c3e03..569af02 100644 --- 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 index c230174..84c5b99 100644 --- 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 index 02eed2e..807738e 100644 --- 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 index d3e8350..d17798f 100755 --- 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 index 78a2fd0..9edfa38 100644 --- 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 index cfe7d9c..887d8ce 100755 --- 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 index 3dba0bc..0274b23 100644 --- 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 index 99901c4..731c31b 100644 --- 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 index f01563b..857b6cb 100644 --- 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 index 36fb418..deb0f44 100755 --- 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 index 9caf9b5..f745df0 100644 --- 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 index df03a05..7db1bef 100644 --- 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 index 6384516..32b40e4 100755 --- 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 index 38eaea2..e5f702a 100644 --- 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 index 219f6a0..41ef271 100644 --- 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 index a4374ba..77c6cac 100644 --- 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 \ No newline at end of file + - 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 \ No newline at end of file