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assemblies.yaml
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name: MosaiCatcher assemblies checks
on:
push:
branches:
- "**"
schedule:
- cron: "0 0 * * 0"
jobs:
Testing-with-hg38:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic-v7
- Testing-basic-with-ashleys
# - Testing-basic-with-slurm
steps:
- 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@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-hg19:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic-v7
- Testing-basic-with-ashleys
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true
- name: Pull LFS objects in submodules
run: git submodule foreach --recursive 'git lfs pull'
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-T2T:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic-v7
- Testing-basic-with-ashleys
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true
- name: Pull LFS objects in submodules
run: git submodule foreach --recursive 'git lfs pull'
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-mm10:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic-v7
- Testing-basic-with-ashleys
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true
- name: Pull LFS objects in submodules
run: git submodule foreach --recursive 'git lfs pull'
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$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==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile