.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
environment.yml
environment_minimal.yml
install_seqnado.sh
mkdocs.yml
pyproject.toml
setup.py
testing.yml
.devcontainer/Dockerfile
.devcontainer/devcontainer.json
.github/dependabot.yml
.github/scripts/generate_environments.py
.github/scripts/update_bioconda_recipe.py
.github/workflows/build_docs.yml
.github/workflows/publish_pypi_release.yml
.github/workflows/test_genome_build.yml
.github/workflows/test_multiomics.yml
.github/workflows/test_pipelines.yml
.github/workflows/test_unit.yml
containers/Dockerfile
containers/docker-compose.yml
containers/ml_cpu/Dockerfile
containers/ml_cpu/seqnado_ml_cpu.def
containers/ml_gpu/seqnado_ml_gpu.def
containers/pipeline/Dockerfile
containers/pipeline/environment_pipeline.yml
containers/pipeline/multiqc_config.yaml
containers/pipeline/seqnado.png
containers/pipeline/seqnado_pipeline.def
docs/SUMMARY.md
docs/citation.md
docs/cli.md
docs/cluster_config.md
docs/configuration.md
docs/design.md
docs/examples.md
docs/faq.md
docs/genomes.md
docs/geo_download.md
docs/index.md
docs/initialisation.md
docs/installation.md
docs/normalisation.md
docs/outputs.md
docs/pipeline.md
docs/quick_start.md
docs/tools.md
docs/troubleshooting.md
docs/api/config.md
docs/api/core.md
docs/api/index.md
docs/api/inputs.md
docs/api/outputs.md
docs/javascripts/mathjax.js
docs/javascripts/toc-collapse.js
docs/scripts/generate_tool_citations.py
docs/scripts/hooks.py
docs/scripts/third_party_tools_config.py
docs/stylesheets/extra.css
seqnado/__init__.py
seqnado/_version.py
seqnado/core.py
seqnado/init.sh
seqnado/utils.py
seqnado.egg-info/PKG-INFO
seqnado.egg-info/SOURCES.txt
seqnado.egg-info/dependency_links.txt
seqnado.egg-info/entry_points.txt
seqnado.egg-info/requires.txt
seqnado.egg-info/top_level.txt
seqnado/cli/__init__.py
seqnado/cli/app.py
seqnado/cli/app_instance.py
seqnado/cli/autocomplete.py
seqnado/cli/data_validation.py
seqnado/cli/multiomics_helpers.py
seqnado/cli/snakemake_builder.py
seqnado/cli/tools_helpers.py
seqnado/cli/utils.py
seqnado/cli/commands/__init__.py
seqnado/cli/commands/config.py
seqnado/cli/commands/design.py
seqnado/cli/commands/download.py
seqnado/cli/commands/genomes.py
seqnado/cli/commands/init.py
seqnado/cli/commands/pipeline.py
seqnado/cli/commands/tools.py
seqnado/config/__init__.py
seqnado/config/configs.py
seqnado/config/core.py
seqnado/config/fastq_screen_generator.py
seqnado/config/geo_submission.py
seqnado/config/mixins.py
seqnado/config/multiomics.py
seqnado/config/third_party_tools.py
seqnado/config/user_input.py
seqnado/data/__init__.py
seqnado/data/config_template.jinja
seqnado/data/deseq2.qmd.jinja
seqnado/data/genomes_template.json
seqnado/data/geo_upload_instructions.txt
seqnado/data/logo.txt
seqnado/data/preset_genomes.json
seqnado/inputs/__init__.py
seqnado/inputs/bam.py
seqnado/inputs/bigwigs.py
seqnado/inputs/core.py
seqnado/inputs/fastq.py
seqnado/inputs/grouping.py
seqnado/inputs/helpers.py
seqnado/inputs/interfaces.py
seqnado/inputs/validation.py
seqnado/outputs/__init__.py
seqnado/outputs/core.py
seqnado/outputs/files.py
seqnado/outputs/multiomics.py
seqnado/tools/__init__.py
seqnado/tools/container_strategies.py
seqnado/tools/tool_citations.bib
seqnado/tools/tools.json
seqnado/tools/tools.py
seqnado/tools/version_parsing.py
seqnado/workflow/Snakefile
seqnado/workflow/Snakefile_genome
seqnado/workflow/Snakefile_multi
seqnado/workflow/__init__.py
seqnado/workflow/envs/profiles/profile_aws/config.yaml
seqnado/workflow/envs/profiles/profile_local_conda/config.yaml
seqnado/workflow/envs/profiles/profile_local_docker/config.yaml
seqnado/workflow/envs/profiles/profile_local_environment/config.yaml
seqnado/workflow/envs/profiles/profile_local_singularity/config.yaml
seqnado/workflow/envs/profiles/profile_slurm_singularity/config.yaml
seqnado/workflow/envs/profiles/profile_test/config.v8+.yaml
seqnado/workflow/helpers/__init__.py
seqnado/workflow/helpers/bam.py
seqnado/workflow/helpers/common.py
seqnado/workflow/helpers/crispr.py
seqnado/workflow/helpers/geo.py
seqnado/workflow/helpers/mcc.py
seqnado/workflow/helpers/multiomics.py
seqnado/workflow/helpers/normalization.py
seqnado/workflow/helpers/peaks.py
seqnado/workflow/helpers/qc.py
seqnado/workflow/helpers/quant.py
seqnado/workflow/helpers/visualise.py
seqnado/workflow/rules/alignment/dna.smk
seqnado/workflow/rules/alignment/rna.smk
seqnado/workflow/rules/bam/all.smk
seqnado/workflow/rules/bam/blacklist.smk
seqnado/workflow/rules/bam/duplicates.smk
seqnado/workflow/rules/bam/filter.smk
seqnado/workflow/rules/bam/index.smk
seqnado/workflow/rules/bam/manipulate.smk
seqnado/workflow/rules/bam/merge.smk
seqnado/workflow/rules/common/utilities.smk
seqnado/workflow/rules/crispr/adapters.smk
seqnado/workflow/rules/crispr/align.smk
seqnado/workflow/rules/crispr/all.smk
seqnado/workflow/rules/crispr/feature_counts.smk
seqnado/workflow/rules/crispr/mageck.smk
seqnado/workflow/rules/crispr/trim.smk
seqnado/workflow/rules/dataset/dataset.smk
seqnado/workflow/rules/dataset/multiomics_dataset.smk
seqnado/workflow/rules/differential/rna.smk
seqnado/workflow/rules/fastq/manipulate.smk
seqnado/workflow/rules/fastq/screen.smk
seqnado/workflow/rules/fastq/trim.smk
seqnado/workflow/rules/genomes/build_index.smk
seqnado/workflow/rules/genomes/download.smk
seqnado/workflow/rules/geo/download.smk
seqnado/workflow/rules/geo/submission.smk
seqnado/workflow/rules/mcc/all.smk
seqnado/workflow/rules/mcc/common.smk
seqnado/workflow/rules/mcc/compare.smk
seqnado/workflow/rules/mcc/identify.smk
seqnado/workflow/rules/mcc/interactions.smk
seqnado/workflow/rules/mcc/map_to_genome.smk
seqnado/workflow/rules/mcc/map_to_viewpoints.smk
seqnado/workflow/rules/mcc/peaks.smk
seqnado/workflow/rules/mcc/pileup.smk
seqnado/workflow/rules/mcc/stats.smk
seqnado/workflow/rules/meth/calling.smk
seqnado/workflow/rules/motifs/motif.smk
seqnado/workflow/rules/multiomics/all.smk
seqnado/workflow/rules/multiomics/assays.smk
seqnado/workflow/rules/multiomics/browser.smk
seqnado/workflow/rules/multiomics/heatmap.smk
seqnado/workflow/rules/multiomics/summary.smk
seqnado/workflow/rules/normalization/merged.smk
seqnado/workflow/rules/normalization/scaling.smk
seqnado/workflow/rules/normalization/spikein.smk
seqnado/workflow/rules/peaks/default.smk
seqnado/workflow/rules/peaks/merge.smk
seqnado/workflow/rules/pileup/common.smk
seqnado/workflow/rules/pileup/dna.smk
seqnado/workflow/rules/pileup/dna_default.smk
seqnado/workflow/rules/pileup/dna_merge_normalized.smk
seqnado/workflow/rules/pileup/dna_merged.smk
seqnado/workflow/rules/pileup/dna_normalized.smk
seqnado/workflow/rules/pileup/rna.smk
seqnado/workflow/rules/pileup/rna_default.smk
seqnado/workflow/rules/pileup/rna_merge_normalized.smk
seqnado/workflow/rules/pileup/rna_merged.smk
seqnado/workflow/rules/pileup/rna_normalized.smk
seqnado/workflow/rules/protocol/protocol.smk
seqnado/workflow/rules/qc/qc.smk
seqnado/workflow/rules/quant/featurecounts.smk
seqnado/workflow/rules/quant/merged.smk
seqnado/workflow/rules/quant/salmon.smk
seqnado/workflow/rules/spikein/all.smk
seqnado/workflow/rules/spikein/dna_spikein.smk
seqnado/workflow/rules/spikein/rna_spikein.smk
seqnado/workflow/rules/spikein/spikein.smk
seqnado/workflow/rules/variant/annotate.smk
seqnado/workflow/rules/variant/call.smk
seqnado/workflow/rules/visualise/browser.smk
seqnado/workflow/rules/visualise/heatmap.smk
seqnado/workflow/rules/visualise/hub.smk
seqnado/workflow/scripts/alignment_stats.py
seqnado/workflow/scripts/calculate_csaw_scaling_factors.py
seqnado/workflow/scripts/calculate_scaling_factors.R
seqnado/workflow/scripts/calculate_spikein_norm_factors.py
seqnado/workflow/scripts/calculate_spikein_norm_factors_deseq.R
seqnado/workflow/scripts/calculate_spikein_norm_factors_edger.R
seqnado/workflow/scripts/calculate_spikein_norm_orlando.py
seqnado/workflow/scripts/create_hub_with_tracknado.py
seqnado/workflow/scripts/create_mageck_design_matrix.py
seqnado/workflow/scripts/deduplicate_fastq.py
seqnado/workflow/scripts/detect_crispr_adapters.py
seqnado/workflow/scripts/get_salmon_counts.py
seqnado/workflow/scripts/mcc_combine_coolers.py
seqnado/workflow/scripts/mcc_split_reads_aligned_to_viewpoints.py
seqnado/workflow/scripts/methylation_conversion.py
seqnado/workflow/scripts/produce_data_processing_protocol.py
seqnado/workflow/scripts/remove_blacklist.py
seqnado/workflow/scripts/run_plotnado.py
seqnado/workflow/scripts/tile_genome.py