From a065ac3532aee3f3d67c76cfe0dab6617141db31 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 5 Dec 2019 16:03:00 +0100 Subject: [PATCH] Actions: install nextflow --- .github/workflows/fastqc.yml | 10 +++++++--- .github/workflows/samtools_index.yml | 10 +++++++--- .github/workflows/samtools_sort.yml | 10 +++++++--- .github/workflows/trim_galore.yml | 10 +++++++--- 4 files changed, 28 insertions(+), 12 deletions(-) diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index fb395797..beeaea5a 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -6,7 +6,7 @@ on: paths: tools/fastqc/* jobs: - run_multiqc: + run_ci_test: runs-on: ubuntu-latest steps: @@ -14,6 +14,10 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + - name: Install Nextflow + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + # Test the module - - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 - run: nextflow run ./tools/fastqc/test/ + - run: nextflow run ./tools/fastqc/test/ diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 32719e5e..fcc26ecf 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -6,7 +6,7 @@ on: paths: tools/samtools/index* jobs: - run_multiqc: + run_ci_test: runs-on: ubuntu-latest steps: @@ -14,6 +14,10 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + - name: Install Nextflow + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + # Test the module - - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 - run: nextflow run ./tools/samtools/index/test/ + - run: nextflow run ./tools/samtools/index/test/ diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index 46791408..c9fa338a 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -6,7 +6,7 @@ on: paths: tools/samtools/sort* jobs: - run_multiqc: + run_ci_test: runs-on: ubuntu-latest steps: @@ -14,6 +14,10 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + - name: Install Nextflow + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + # Test the module - - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 - run: nextflow run ./tools/samtools/sort/test/ + - run: nextflow run ./tools/samtools/sort/test/ diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml index 48c93b5f..437cc12c 100644 --- a/.github/workflows/trim_galore.yml +++ b/.github/workflows/trim_galore.yml @@ -6,7 +6,7 @@ on: paths: tools/trim_galore/* jobs: - run_multiqc: + run_ci_test: runs-on: ubuntu-latest steps: @@ -14,6 +14,10 @@ jobs: # Check out the repository - uses: actions/checkout@v1 + - name: Install Nextflow + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + # Test the module - - uses: docker://quay.io/biocontainers/nextflow:19.10.0--hecc5488_0 - run: nextflow run ./tools/trim_galore/test/ + - run: nextflow run ./tools/trim_galore/test/