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Test with ashleys, update GH actions without LFS #173

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Test with ashleys, update GH actions without LFS

Test with ashleys, update GH actions without LFS #173

Workflow file for this run

.github/workflows/assemblies.yaml at f66e52c
name: MosaiCatcher assemblies checks
on:
push:
branches:
- "**"
schedule:
- cron: "0 0 * * 0"
jobs:
Testing-with-hg38:

Check failure on line 11 in .github/workflows/assemblies.yaml

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The workflow is not valid. .github/workflows/assemblies.yaml (Line: 11, Col: 3): The workflow must contain at least one job with no dependencies.
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: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-hg19:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic-v7
- Testing-basic-with-ashleys
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-T2T:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic-v7
- Testing-basic-with-ashleys
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-mm10:
runs-on: ubuntu-latest
needs:
- Formatting
- Linting
- Testing-basic-v7
- Testing-basic-with-ashleys
# - Testing-basic-with-slurm
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true
- name: Git Submodule Update
run: |
git pull --recurse-submodules
git submodule update --remote --recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$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