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MosaiCatcher basic checks

Missing storage plugin dependencie #33

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Missing storage plugin dependencie

Missing storage plugin dependencie #33

Workflow file for this run

.github/workflows/main_test.yaml at bddb8d1
name: MosaiCatcher basic checks
on:
push:
branches:
- "**"
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:
- name: Checkout repository with submodules
uses: actions/checkout@v4
with:
submodules: "recursive" # Ensures all submodules are checked out
lfs: true # Ensures LFS objects for the main repo are pulled
- name: Pull LFS objects in submodules
run: |
git submodule foreach --recursive 'git lfs pull'
- name: List contents of .tests
run: |
tree -h .tests
- name: List contents of workflow/data
run: |
tree -h workflow/data
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: |
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install -c conda-forge mamba
- name: Setup snakemake
run: |
mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
- name: Run Snakemake Lint
run: |
snakemake --lint
Testing-basic:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
steps:
- name: Checkout repository with submodules and LFS
uses: actions/checkout@v4
with:
submodules: recursive
lfs: true
- name: Pull LFS objects in submodules
run: git submodule foreach --recursive 'git lfs pull'
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: List contents of .tests
run: |
tree -h .tests
- name: Show config file
run: |
cat .tests/config/simple_config_mosaicatcher.yaml
- name: List contents of workflow/data
run: |
tree -h workflow/data
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --sdm conda --configfile .tests/config/simple_config_mosaicatcher.yaml \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-basic-with-ashleys:
# runs-on: ubuntu-latest
# # needs:
# # - Formatting
# # - Linting
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: List contents of .tests
# run: |
# tree -h .tests
# - name: Show config file
# run: |
# cat .tests/config/simple_config_mosaicatcher.yaml
# - name: List contents of workflow/data
# run: |
# tree -h workflow/data
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config ashleys_pipeline=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-MultiQC:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config MultiQC=True ashleys_pipeline=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-ms-norm:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config multistep_normalisation=True ashleys_pipeline=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-breakpointR-only:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config breakpointR=True breakpointR_only=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-whatshap-only:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config whatshap_only=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-hg38:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# # - Testing-basic-with-slurm
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-hg19:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# # - Testing-basic-with-slurm
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-T2T:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# # - Testing-basic-with-slurm
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$CONDA/bin" >> $GITHUB_PATH
# - name: Install dependencies
# run: conda install -c conda-forge mamba
# - name: Setup Snakemake
# run: mamba install -c conda-forge -c bioconda snakemake snakemake-storage-plugin-http
# - name: List options of workflow
# run: |
# snakemake --cores 1 --config list_commands=True --verbose --debug
# - name: Run workflow
# run: |
# snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \
# --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
# Testing-with-mm10:
# runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic
# - Testing-basic-with-ashleys
# # - Testing-basic-with-slurm
# steps:
# - name: Checkout repository with submodules and LFS
# uses: actions/checkout@v4
# with:
# submodules: recursive
# lfs: true
# - name: Pull LFS objects in submodules
# run: git submodule foreach --recursive 'git lfs pull'
# - name: Setup Python
# uses: actions/setup-python@v5
# with:
# python-version: "3.12"
# - name: Add Conda to system path
# run: echo "$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 snakemake-storage-plugin-http
# - 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