.gitignore
.gitlab-ci.yml
AUTHORS.md
LICENCE
README.rst
codemeta.json
pyproject.toml
readthedocs.yml
docs/Makefile
docs/requirements.txt
docs/source/authors_contrib.rst
docs/source/conf.py
docs/source/edit_profile.rst
docs/source/index.rst
docs/source/install.rst
docs/source/intersect.rst
docs/source/kmer_assembly.rst
docs/source/kmer_gwas.rst
docs/source/lfmm.rst
docs/source/licence.rst
docs/source/mapping.rst
docs/source/modules.rst
docs/source/output.rst
docs/source/pcadapt.rst
docs/source/results.rst
docs/source/rules.rst
docs/source/run_test.rst
docs/source/section.rst
docs/source/snmf.rst
docs/source/_static/ikiss.jpg
docs/source/_static/ikiss.png
docs/source/_static/ikiss_name.jpg
docs/source/_static/ikiss_name.png
docs/source/_static/ird_small.png
docs/source/_static/logo_ikiss.jpg
docs/source/_static/logo_ikiss.png
ikiss/Snakefile
ikiss/__init__.py
ikiss/_version.py
ikiss/global_variables.py
ikiss/logo_ikiss.png
ikiss/main.py
ikiss/module.py
ikiss.egg-info/PKG-INFO
ikiss.egg-info/SOURCES.txt
ikiss.egg-info/dependency_links.txt
ikiss.egg-info/entry_points.txt
ikiss.egg-info/requires.txt
ikiss.egg-info/top_level.txt
ikiss/containers/Dockerfile
ikiss/containers/Singularity.ikiss_tools.def
ikiss/img/ird_small.png
ikiss/img/schema_pipeline_dag.pdf
ikiss/img/schema_pipeline_global1.pdf
ikiss/img/schema_pipeline_global2.pdf
ikiss/install_files/config.yaml
ikiss/install_files/configfile.yaml
ikiss/install_files/tools_path.yaml
ikiss/notebooks/extract_clima.ipynb
ikiss/notebooks/manhattan_plot_example.ipynb
ikiss/notebooks/snmf_manipulation.qmd
ikiss/snakemake_scripts/generate_tools.py
ikiss/snakemake_scripts/get_versions.py
ikiss/snakemake_scripts/kmer-bed2fasta.py
ikiss/snakemake_scripts/lfmm.R
ikiss/snakemake_scripts/outliers_and_position.py
ikiss/snakemake_scripts/pca_from_phenotype.py
ikiss/snakemake_scripts/pcadapt.R
ikiss/snakemake_scripts/report.py
ikiss/snakemake_scripts/run_ikiss.sbatch
ikiss/snakemake_scripts/snmf.R
ikiss/snakemake_scripts/split_bed.py
ikiss/snakemake_scripts/stats_intersect.py
ikiss/snakemake_scripts/report_template/_quarto.yml
ikiss/snakemake_scripts/report_template/cellalina.csl
ikiss/snakemake_scripts/report_template/index.qmd
ikiss/snakemake_scripts/report_template/logo_ikiss.png
ikiss/snakemake_scripts/report_template/references.bib
ikiss/snakemake_scripts/report_template/references.qmd
ikiss/snakemake_scripts/report_template/versions.csv
ikiss/useful_scripts/.gitkeep
ikiss/useful_scripts/jaccard_from_csv.py
ikiss/useful_scripts/plotting_jaccard_by_pop.html
ikiss/useful_scripts/plotting_jaccard_by_pop.ipynb
ikiss/useful_scripts/run_jaccard.sh