From 1dcd1456f63a44dc1cc7ccbf147d456d4722e13a Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Mon, 29 Apr 2024 17:42:54 -0300 Subject: [PATCH] add git action --- .github/workflows/test_pr_nanopore_docker.yml | 77 +++++++++------- .../test_pr_nanopore_singularity.yml | 87 +++++++++++-------- 2 files changed, 93 insertions(+), 71 deletions(-) diff --git a/.github/workflows/test_pr_nanopore_docker.yml b/.github/workflows/test_pr_nanopore_docker.yml index 4bb58d4..4b84486 100644 --- a/.github/workflows/test_pr_nanopore_docker.yml +++ b/.github/workflows/test_pr_nanopore_docker.yml @@ -7,8 +7,8 @@ name: Testing nanopore / docker from PR on: pull_request: - branches: [ master, dev ] - types: [ opened, synchronize, reopened ] + branches: [master, dev] + types: [opened, synchronize, reopened] jobs: run_nextflow: @@ -17,35 +17,46 @@ jobs: env: DOCKERHUB_USERNAME: ${{ secrets.DOCKER_USER }} DOCKERHUB_PASS: ${{ secrets.DOCKER_PASSWORD }} - + steps: - - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - - name: Clean environment - run: | - sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android - sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET - - - name: Run tests for nanopore - run: | - wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_ont_15X.fastq.gz - nextflow run main.nf \ - -profile docker \ - --max_cpus 2 \ - --output TEST_DIR \ - --nanopore_fastq "ecoli_ont_15X.fastq.gz" - rm -r work .nextflow* - - - name: View results - run: | - sudo apt-get install -y tree - tree TEST_DIR + + - name: Check out pipeline code + uses: actions/checkout@v2 + + - name: Install Nextflow + env: + CAPSULE_LOG: none + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Clean environment + run: | + sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android + sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET + + - name: Run tests for nanopore + run: | + wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_ont_15X.fastq.gz + nextflow run main.nf \ + -profile docker \ + --max_cpus 2 \ + --output TEST_DIR \ + --nanopore_fastq "ecoli_ont_15X.fastq.gz" + rm -r work .nextflow* + + - name: Run tests for nanopore (ABI) + run: | + wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_ont_15X.fastq.gz + nextflow run main.nf \ + -profile docker \ + --max_cpus 2 \ + --output TEST_DIR \ + --nanopore_fastq "ecoli_ont_15X.fastq.gz" \ + --use_porechop_abi + rm -r work .nextflow* + + - name: View results + run: | + sudo apt-get install -y tree + tree TEST_DIR diff --git a/.github/workflows/test_pr_nanopore_singularity.yml b/.github/workflows/test_pr_nanopore_singularity.yml index aef2aab..3f0a61a 100644 --- a/.github/workflows/test_pr_nanopore_singularity.yml +++ b/.github/workflows/test_pr_nanopore_singularity.yml @@ -7,8 +7,8 @@ name: Testing nanopore / singularity from PR on: pull_request: - branches: [ master, dev ] - types: [ opened, synchronize, reopened ] + branches: [master, dev] + types: [opened, synchronize, reopened] jobs: run_nextflow: @@ -17,40 +17,51 @@ jobs: env: DOCKERHUB_USERNAME: ${{ secrets.DOCKER_USER }} DOCKERHUB_PASS: ${{ secrets.DOCKER_PASSWORD }} - + steps: - - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Singularity - uses: eWaterCycle/setup-singularity@v7 - with: - singularity-version: 3.8.3 - - - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - - name: Clean environment - run: | - sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android - sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET - - - name: Run tests for nanopore - run: | - wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_ont_15X.fastq.gz - nextflow run main.nf \ - -profile singularity \ - --max_cpus 2 \ - --output TEST_DIR \ - --nanopore_fastq "ecoli_ont_15X.fastq.gz" - rm -r work .nextflow* - - - name: View results - run: | - sudo apt-get install -y tree - tree TEST_DIR + + - name: Check out pipeline code + uses: actions/checkout@v2 + + - name: Install Singularity + uses: eWaterCycle/setup-singularity@v7 + with: + singularity-version: 3.8.3 + + - name: Install Nextflow + env: + CAPSULE_LOG: none + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Clean environment + run: | + sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android + sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET + + - name: Run tests for nanopore + run: | + wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_ont_15X.fastq.gz + nextflow run main.nf \ + -profile singularity \ + --max_cpus 2 \ + --output TEST_DIR \ + --nanopore_fastq "ecoli_ont_15X.fastq.gz" + rm -r work .nextflow* + + - name: Run tests for nanopore (ABI) + run: | + wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_ont_15X.fastq.gz + nextflow run main.nf \ + -profile singularity \ + --max_cpus 2 \ + --output TEST_DIR \ + --nanopore_fastq "ecoli_ont_15X.fastq.gz" \ + --use_porechop_abi + rm -r work .nextflow* + + - name: View results + run: | + sudo apt-get install -y tree + tree TEST_DIR