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MosaiCatcher advanced modules checks

MosaiCatcher advanced modules checks #23

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MosaiCatcher advanced modules checks

MosaiCatcher advanced modules checks #23

Workflow file for this run

.github/workflows/advanced.yaml at 2b6921d
name: MosaiCatcher advanced modules checks
on:
workflow_dispatch:
inputs:
logLevel:
description: "Log level"
required: true
default: "warning"
type: choice
options:
- info
- warning
- debug
schedule:
- cron: "0 0 * * 0"
jobs:
Testing-with-MultiQC:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic-v7
# - Testing-basic-with-ashleys
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v4
with:
submodules: recursive
# lfs: true
- name: Git Submodule Update
run: |
# git pull --recurse-submodules
git submodule update --remote --recursive --force --init
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config MultiQC=True ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-ms-norm:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic-v7
# - Testing-basic-with-ashleys
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v4
with:
submodules: recursive
# lfs: true
- name: Git Submodule Update
run: |
# git pull --recurse-submodules
git submodule update --remote --recursive --force --init
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config multistep_normalisation=True ashleys_pipeline=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-breakpointR-only:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic-v7
# - Testing-basic-with-ashleys
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v4
with:
submodules: recursive
# lfs: true
- name: Git Submodule Update
run: |
# git pull --recurse-submodules
git submodule update --remote --recursive --force --init
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install dependencies
run: conda install -c conda-forge mamba
- name: Setup Snakemake
run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
- name: List options of workflow
run: |
snakemake --cores 1 --config list_commands=True --verbose --debug
- name: Run workflow
run: |
snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config breakpointR=True breakpointR_only=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
Testing-with-whatshap-only:
runs-on: ubuntu-latest
# needs:
# - Formatting
# - Linting
# - Testing-basic-v7
# - Testing-basic-with-ashleys
steps:
- name: Checkout repository with submodules
uses: actions/checkout@v4
with:
submodules: recursive
# lfs: true
- name: Git Submodule Update
run: |
# git pull --recurse-submodules
git submodule update --remote --recursive --force --init
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Add Conda to system path
run: echo "$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 --configfile .tests/config/simple_config_mosaicatcher.yaml --config whatshap_only=True \
--conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile