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Actions: install nextflow

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This commit is contained in:
Phil Ewels 2019-12-05 16:03:00 +01:00
parent acc4eb0054
commit a065ac3532
4 changed files with 28 additions and 12 deletions
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10
.github/workflows/fastqc.yml vendored
View file

@ -6,7 +6,7 @@ on:
paths: tools/fastqc/* paths: tools/fastqc/*
jobs: jobs:
run_multiqc: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
steps: steps:
@ -14,6 +14,10 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
# Test the module # 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/

10
.github/workflows/samtools_index.yml vendored
View file

@ -6,7 +6,7 @@ on:
paths: tools/samtools/index* paths: tools/samtools/index*
jobs: jobs:
run_multiqc: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
steps: steps:
@ -14,6 +14,10 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
# Test the module # 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/

10
.github/workflows/samtools_sort.yml vendored
View file

@ -6,7 +6,7 @@ on:
paths: tools/samtools/sort* paths: tools/samtools/sort*
jobs: jobs:
run_multiqc: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
steps: steps:
@ -14,6 +14,10 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
# Test the module # 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/

10
.github/workflows/trim_galore.yml vendored
View file

@ -6,7 +6,7 @@ on:
paths: tools/trim_galore/* paths: tools/trim_galore/*
jobs: jobs:
run_multiqc: run_ci_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
steps: steps:
@ -14,6 +14,10 @@ jobs:
# Check out the repository # Check out the repository
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
# Test the module # 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/