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3t-seq test run

chore(main): release 1.0.1 #50

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chore(main): release 1.0.1

chore(main): release 1.0.1 #50

Workflow file for this run

.github/workflows/main.yml at f794d22
name: 3t-seq test run
on:
release:
types: [ published ]
pull_request:
branches-ignore: []
jobs:
formatting:
runs-on: ubuntu-latest
steps:
- name: Checkout with submodules
uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Formatting
uses: github/super-linter@v5
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: main
GITHUB_TOKEN: ${{ secrets.TOKEN }}
VALIDATE_SNAKEMAKE_SNAKEFMT: true
linting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Linting
uses: snakemake/snakemake-github-action@v1.22.0
with:
directory: tests
snakefile: workflow/Snakefile
args: "--configfile tests/config.yaml --lint"
run-workflow-complete:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v3
with:
submodules: recursive
lfs: true
- name: Setup Python 3.11
uses: actions/setup-python@v2
with:
python-version: 3.11
- name: Add Conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install -c conda-forge mamba
- name: Setup snakemake
run: |
mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
- name: Run workflow
run: |
snakemake --directory tests --configfile tests/config.yaml --profile tests/profile --snakefile workflow/Snakefile
run-workflow-no-te:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v3
with:
submodules: recursive
lfs: true
- name: Setup Python 3.11
uses: actions/setup-python@v2
with:
python-version: 3.11
- name: Add Conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install -c conda-forge mamba
- name: Setup snakemake
run: |
mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
- name: Run workflow
run: |
snakemake --directory tests --configfile tests/config-no-te.yaml --profile tests/profile --snakefile workflow/Snakefile
run-workflow-no-trna:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v3
with:
submodules: recursive
lfs: true
- name: Setup Python 3.11
uses: actions/setup-python@v2
with:
python-version: 3.11
- name: Add Conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install -c conda-forge mamba
- name: Setup snakemake
run: |
mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
- name: Run workflow
run: |
snakemake --directory tests --configfile tests/config-no-trna.yaml --profile tests/profile --snakefile workflow/Snakefile
run-workflow-no-trna-te:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v3
with:
submodules: recursive
lfs: true
- name: Setup Python 3.11
uses: actions/setup-python@v2
with:
python-version: 3.11
- name: Add Conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install -c conda-forge mamba
- name: Setup snakemake
run: |
mamba install -c conda-forge -c bioconda snakemake=7.28.3 singularity
- name: Run workflow
run: |
snakemake --directory tests --configfile tests/config-no-trna-te.yaml --profile tests/profile --snakefile workflow/Snakefile