added tests to reduce errors on release

UPHL-BioNGS · Mar 2, 2023 · 69408e5 · 69408e5
1 parent fb13895
commit 69408e5
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diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml
@@ -0,0 +1,41 @@
+name: Test Grandeur workflow with E. coli and Shigella
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        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: |
+          docker --version
+          
+          mkdir fastas 
+
+          for accesion in GCA_009738455.1_ASM973845v1 GCA_003019175.1_ASM301917v1 GCA_023823105.1_ASM2382310v1
+          do
+            all=$(echo $accession | cut -f 2 -d "_")
+            fir=$(echo $all | cut -c 1-3)
+            mid=$(echo $all | cut -c 4-6)
+            end=$(echo $all | cut -c 7-9)
+            wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$fir/$mid/$end/$accession/${accession}_genomic.fna.gz
+            gzip -d ${accession}_genomic.fna.gz
+            mv ${accession}_genomic.fna fastas/.
+          done
+
+          nextflow run . -profile docker --maxcpus 2 --medcpus 2
+          cat grandeur/grandeur_summary.tsv
diff --git a/.github/workflows/just_msa.yml b/.github/workflows/just_msa.yml
@@ -0,0 +1,36 @@
+name: Test Grandeur just_msa workflow
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        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: |
+          docker --version
+
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/863/225/GCA_904863225.1_KSB1_6J/GCA_904863225.1_KSB1_6J_genomic.fna.gz           && gzip -d GCA_904863225.1_KSB1_6J_genomic.fna.gz
+          
+          mkdir fastas
+          mv *fna fastas/.
+
+          nextflow run . -profile docker,just_msa --maxcpus 2 --medcpus 2
diff --git a/.github/workflows/phylogenetic_workflow.yml b/.github/workflows/phylogenetic_workflow.yml
@@ -0,0 +1,41 @@
+name: Test Grandeur phylogenetic workflow
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        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: |
+          docker --version
+
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/863/225/GCA_904863225.1_KSB1_6J/GCA_904863225.1_KSB1_6J_genomic.fna.gz           && gzip -d GCA_904863225.1_KSB1_6J_genomic.fna.gz
+          
+          mkdir fastas
+          mv *fna fastas/.
+
+          nextflow run . -profile docker --maxcpus 2 --medcpus 2
+
+          cat grandeur/grandeur_summary.tsv
+
+          nextflow run . -profile docker,msa --maxcpus 2 --medcpus 2 -resume
+          
diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml
@@ -0,0 +1,40 @@
+name: Test Grandeur workflow with salmonella
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        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: |
+          docker --version
+          
+          mkdir fastas
+          for accesion in GCA_019710395.3_ASM1971039v3 GCA_001652385.2_ASM165238v2 GCA_013344545.1_ASM1334454v1
+          do
+            all=$(echo $accession | cut -f 2 -d "_")
+            fir=$(echo $all | cut -c 1-3)
+            mid=$(echo $all | cut -c 4-6)
+            end=$(echo $all | cut -c 7-9)
+            wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$fir/$mid/$end/$accession/${accession}_genomic.fna.gz
+            gzip -d ${accession}_genomic.fna.gz
+            mv ${accession}_genomic.fna fastas/.
+          done
+
+          nextflow run . -profile docker --maxcpus 2 --medcpus 2
+          cat grandeur/grandeur_summary.tsv
diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml
@@ -0,0 +1,40 @@
+name: Test Grandeur workflow with vibrio
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: Checkout LFS objects
+        run: git lfs checkout
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+          
+      - name: Run Grandeur
+        run: |
+          docker --version
+          
+          mkdir fastas
+          for accesion in GCA_009665515.2_ASM966551v2 GCA_009763645.1_ASM976364v1 GCA_004355205.1_ASM435520v1 GCA_009665315.1_ASM966531v1 GCA_002953375.1_ASM295337v1
+          do
+            all=$(echo $accession | cut -f 2 -d "_")
+            fir=$(echo $all | cut -c 1-3)
+            mid=$(echo $all | cut -c 4-6)
+            end=$(echo $all | cut -c 7-9)
+            wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$fir/$mid/$end/$accession/${accession}_genomic.fna.gz
+            gzip -d ${accession}_genomic.fna.gz
+            mv ${accession}_genomic.fna fastas/.
+          done
+
+          nextflow run . -profile docker --maxcpus 2 --medcpus 2
+          cat grandeur/grandeur_summary.tsv
diff --git a/.github/workflows/withoutfastani.yml b/.github/workflows/withoutfastani.yml
@@ -0,0 +1,40 @@
+name: Test Grandeur withoutfastani workflow
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        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: |
+          docker --version
+
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
+          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/863/225/GCA_904863225.1_KSB1_6J/GCA_904863225.1_KSB1_6J_genomic.fna.gz           && gzip -d GCA_904863225.1_KSB1_6J_genomic.fna.gz
+          
+          mkdir fastas
+          mv *fna fastas/.
+
+          nextflow run . -profile docker --maxcpus 2 --medcpus 2
+
+          cat grandeur/grandeur_summary.tsv
+
+          nextflow run . -profile docker,msa --maxcpus 2 --medcpus 2 -resume --current_datastets false --fastani_include false