.gitignore
.gitlab-ci.yml
.readthedocs.yaml
.release.yml
CHANGELOG.md
LICENCE
README.rst
RattleSNP
pyproject.toml
docs/Makefile
docs/requirements.txt
docs/source/ABOUT.rst
docs/source/FAQ.rst
docs/source/INSTALL.rst
docs/source/PROJECT.rst
docs/source/WORKFLOWS.rst
docs/source/click.rst
docs/source/conf.py
docs/source/index.rst
docs/source/_images/rattleSNP-small.svg
docs/source/_images/rattleSNP_logo.png
docs/source/_images/rattleSNP_logo.svg
docs/source/_images/schema_pipeline_global-BUILD_STATS.png
docs/source/_images/schema_pipeline_global-FILTER.png
docs/source/_images/schema_pipeline_global-NOBUILD_STATS.png
docs/source/_images/schema_pipeline_global-SNPCALLING.png
docs/source/_images/schema_pipeline_global.png
docs/source/_static/logo.css
rattleSNP/VERSION
rattleSNP/__init__.py
rattleSNP/_version.py
rattleSNP/global_variables.py
rattleSNP/main.py
rattleSNP/rattleSNP-complete.sh
rattleSNP/rattleSNP_logo.png
rattleSNP/snakemake_module.py
rattleSNP.egg-info/PKG-INFO
rattleSNP.egg-info/SOURCES.txt
rattleSNP.egg-info/dependency_links.txt
rattleSNP.egg-info/entry_points.txt
rattleSNP.egg-info/requires.txt
rattleSNP.egg-info/top_level.txt
rattleSNP/containers/Dockerfile_test
rattleSNP/containers/Singularity.rattleSNP_tools.def
rattleSNP/containers/Singularity.report.def
rattleSNP/default_profile/CookieCutter.py
rattleSNP/default_profile/slurm-sidecar.py
rattleSNP/default_profile/slurm-status.py
rattleSNP/default_profile/slurm-submit.py
rattleSNP/default_profile/slurm_utils.py
rattleSNP/install_files/cluster_config_SLURM.yaml
rattleSNP/install_files/config.yaml
rattleSNP/install_files/tools_path.yaml
rattleSNP/install_files/config_test/config_CMSR.yaml
rattleSNP/scripts/__init__.py
rattleSNP/scripts/vcf2geno.py
rattleSNP/scripts/vcf2phylip.py
rattleSNP/snakefiles/Snakefile
rattleSNP/snakefiles/mapping_stat.snake
rattleSNP/snakemake_scripts/rattleSNP_module.py
rattleSNP/snakemake_scripts/report.Rmd
rattleSNP/snakemake_scripts/report_vcf.Rmd