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main_test.yaml test
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@weber8thomas
weber8thomas committed Jun 19, 2024
1 parent 5254ff2 commit 15223b0
Showing 1 changed file with 92 additions and 125 deletions.
217 changes: 92 additions & 125 deletions .github/workflows/main_test.yaml
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- "**"

jobs:

Formatting:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4

- name: Formatting using Super-Linter
uses: github/super-linter@v4
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: master
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
VALIDATE_SNAKEMAKE_SNAKEFMT: true


Linting:
runs-on: ubuntu-latest
steps:
Expand Down Expand Up @@ -46,109 +62,87 @@ jobs:
run: |
snakemake --lint
Testing-basic:
runs-on: ubuntu-latest
depends-on:
- Formatting
- Linting
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true

# Testing_ashleys_with_custom_python:
# # runs-on: self-hosted
# runs-on: ubuntu-latest
# steps:
# - name: Checkout repository with submodules and lfs
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Setup Python
# uses: actions/setup-python@v2
# - 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 snakemake-storage-plugin-http
# - name: Run workflow
# run: |
# snakemake --cores 1 --software-deployment-method conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

# Setting_slurm_cluster:
# runs-on: ubuntu-latest
# # For the action to work, you have to supply a mysql
# # service as defined below.
# services:
# mysql:
# image: mysql:8.0
# env:
# MYSQL_ROOT_PASSWORD: root
# ports:
# - "8888:3306"
# options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
# steps:
# - uses: actions/checkout@v3
- name: Pull LFS objects in submodules
run: git submodule foreach --recursive 'git lfs pull'

# - uses: koesterlab/setup-slurm-action@v1
- name: Setup Python
uses: actions/setup-python@v2

# - name: Checkout repository with submodules and lfs
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Setup Python
# uses: actions/setup-python@v2
# - 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 snakemake-storage-plugin-http snakemake-executor-plugin-slurm
# - name: Run workflow
# run: |
# snakemake -j 1 -c 4 --executor slurm --workflow-profile .tests/config/slurm_config/ --software-deployment-method conda --conda-frontend mamba --configfile .tests/config/simple_config.yaml -p --snakefile workflow/Snakefile

# WORK
# Formatting:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH

# - name: Formatting
# uses: github/super-linter@v4
# env:
# VALIDATE_ALL_CODEBASE: false
# DEFAULT_BRANCH: master
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# VALIDATE_SNAKEMAKE_SNAKEFMT: true
- name: Install dependencies
run: conda install -c conda-forge mamba

# Linting:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
# - name: Linting
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--lint --config ashleys_pipeline=True"
# Testing_ashleys:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
# - name: Testing data
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# stagein: "conda config --set channel_priority flexible"
# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
# - name: Testing report
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba --report report.zip"
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http

- name: Run workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --software-deployment-method conda --configfile .tests/config/simple_config.yaml \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-basic-with-slurm:
runs-on: ubuntu-latest
depends-on:
- Formatting
- Linting
- Testing-basic
services:
mysql:
image: mysql:8.0
env:
MYSQL_ROOT_PASSWORD: root
ports:
- "8888:3306"
options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3

steps:
- uses: actions/checkout@v3

- uses: koesterlab/setup-slurm-action@v1

- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true

- name: Pull LFS objects in submodules
run: git submodule foreach --recursive 'git lfs pull'

- name: Setup Python
uses: actions/setup-python@v2

- 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 with SLURM support
run: mamba install -c conda-forge -c bioconda snakemake snakemake-executor-plugin-slurm

- name: Run workflow on SLURM
run: |
snakemake -j 1 -c 1 --executor slurm --workflow-profile .tests/config/slurm_config/ --verbose --debug \
--software-deployment-method conda --conda-frontend mamba --configfile .tests/config/simple_config.yaml -p --snakefile workflow/Snakefile
# Testing_ashleys_fastqc_enabled:
# runs-on: ubuntu-latest
Expand Down Expand Up @@ -253,23 +247,6 @@ jobs:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--cores 1 --use-conda --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
# Testing_jub_nb:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
# - name: Testing data
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# stagein: "conda config --set channel_priority flexible"
# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba -p --verbose --debug"
# - name: Testing report
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config hand_selection=True --conda-frontend mamba --report report.zip"
# Testing_publishdir:
# runs-on: ubuntu-latest
# steps:
Expand All @@ -287,13 +264,3 @@ jobs:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"
# Testing_list_commands:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
# - name: Testing data
# uses: snakemake/snakemake-github-action@v1.24.0
# with:
# directory: .
# snakefile: ./workflow/Snakefile
# args: "--cores 1 --config list_commands=True --verbose --debug"

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