Merge pull request #9 from UPHL-BioNGS/erin-dev

Erin dev

.github/workflows/github_actions.config

@@ -0,0 +1,53 @@
+process {
+  withName:unicycler{
+    cpus = 2
+  }
+  withName:flye{
+    cpus = 2
+  }
+  withName:masurca{
+    cpus = 2
+  }
+  withName:medaka{
+    cpus = 2
+  }
+  withName:nanoplot{
+    cpus = 2
+  }
+  withName:miniasm{
+    cpus = 2
+  }
+  withName:porechop{
+    cpus = 2
+  }
+  withName:rasusa{
+    cpus = 2
+  }
+  withName:raven{
+    cpus = 2
+  }
+  withName:'trycycler.*'{
+    cpus = 2
+  }
+  withName:cluster {
+    cpus = 2
+  }
+  withName:reconcile{
+    cpus = 2
+  }
+  withName:msa {
+    cpus = 2
+  } 
+  withName:partition {
+    cpus = 2
+  }
+  withName:consensus {
+    cpus = 2
+  } 
+  withName:combine {
+    cpus = 2
+  } 
+  withName:unicycler {
+    cpus = 2
+  } 
+}

.github/workflows/github_actions_hd_hybrid_sample_sheet.txt

@@ -0,0 +1,2 @@
+sample,fastq,fastq_1,fastq_2
+test,long_reads_high_depth.fastq.gz,short_reads_1.fastq.gz,short_reads_2.fastq.gz

.github/workflows/github_actions_hd_sample_sheet.txt

@@ -0,0 +1,2 @@
+sample,fastq,fastq_1,fastq_2
+test,long_reads_high_depth.fastq.gz,,

.github/workflows/github_actions_hybrid_sample_sheet.txt

@@ -0,0 +1,2 @@
+sample,fastq,fastq_1,fastq_2
+test,long_reads_low_depth.fastq.gz,short_reads_1.fastq.gz,short_reads_2.fastq.gz

.github/workflows/github_actions_sample_sheet.txt

@@ -0,0 +1,2 @@
+sample,fastq
+test,long_reads_low_depth.fastq.gz

.github/workflows/run_workflow_flye.yml

@@ -0,0 +1,29 @@
+name: Test Donut Falls flye assembly
+
+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 Donut Falls
+        run: |
+          docker --version
+          
+          nextflow run . -profile docker,test -c .github/workflows/github_actions.config
+
+          tree donut_falls

.github/workflows/run_workflow_masurca.yml

@@ -0,0 +1,34 @@
+name: Test Donut Falls masurca hybrid assembly
+
+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 Donut Falls
+        run: |
+          docker --version
+          
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz
+          #wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_high_depth.fastq.gz
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz
+
+          #nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/github_actions_hybrid_sample_sheet.txt --assembler masurca
+
+          #tree donut_falls

.github/workflows/run_workflow_miniasm.yml

@@ -0,0 +1,29 @@
+name: Test Donut Falls miniasm and minipolish assembly
+
+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 Donut Falls
+        run: |
+          docker --version
+
+          nextflow run . -profile docker,test3 -c .github/workflows/github_actions.config
+
+          tree donut_falls

.github/workflows/run_workflow_porechop.yml

@@ -0,0 +1,29 @@
+name: Test Donut Falls flye assembly with porechop
+
+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 Donut Falls
+        run: |
+          docker --version
+          
+          nextflow run . -profile docker,test1 -c .github/workflows/github_actions.config
+
+          tree donut_falls

.github/workflows/run_workflow_raven.yml

@@ -0,0 +1,29 @@
+name: Test Donut Falls raven assembly
+
+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 Donut Falls
+        run: |
+          docker --version
+          
+          nextflow run . -profile docker,test2 -c .github/workflows/github_actions.config
+          tree donut_falls
+          

.github/workflows/run_workflow_raven_dir.yml

@@ -0,0 +1,34 @@
+name: Test Donut Falls raven assembly from directory
+
+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 Donut Falls
+        run: |
+          docker --version
+
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_high_depth.fastq.gz
+
+          mkdir reads
+          mv long_reads_high_depth.fastq.gz reads/.
+
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --reads reads --assembler raven
+
+          tree donut_falls

.github/workflows/run_workflow_raven_polish.yml

@@ -0,0 +1,33 @@
+name: Test Donut Falls raven assembly with polishing
+
+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 Donut Falls
+        run: |
+          docker --version
+          
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_high_depth.fastq.gz
+
+          #nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/github_actions_hd_hybrid_sample_sheet.txt --assembler raven
+
+          #tree donut_falls

.github/workflows/run_workflow_trycycler.yml

@@ -0,0 +1,28 @@
+name: Test Donut Falls with trycycler
+
+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 Donut Falls
+        run: |
+          docker --version
+
+          nextflow run . -profile docker,test5 -c .github/workflows/github_actions.config
+          tree donut_falls

.github/workflows/run_workflow_unicycler.yml

@@ -0,0 +1,36 @@
+name: Test Donut Falls unicycler hybrid assembly
+
+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 Donut Falls
+        run: |
+          docker --version
+          
+          mkdir reads
+          # from unicycler test data
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz
+          #wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_high_depth.fastq.gz
+          wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz
+
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet .github/workflows/github_actions_hybrid_sample_sheet.txt --assembler unicycler
+
+          tree donut_falls

.github/workflows/run_workflow_unicyclerlr.yml

@@ -0,0 +1,29 @@
+name: Test Donut Falls unicycler long read only assembly
+
+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 Donut Falls
+        run: |
+          docker --version
+
+          nextflow run . -profile docker,test4 -c .github/workflows/github_actions.config
+          tree donut_falls
+