LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
viralconseq/__init__.py
viralconseq/_orchestrator.py
viralconseq/clair3_models.py
viralconseq/cli.py
viralconseq/config_generator.py
viralconseq/consensus.py
viralconseq/consensus_cli.py
viralconseq/constants.py
viralconseq/create_samplesheet.py
viralconseq/exceptions.py
viralconseq/integrity.py
viralconseq/logging_config.py
viralconseq/provenance.py
viralconseq/reference_splitter.py
viralconseq/report.py
viralconseq/report_cli.py
viralconseq/rerun_cli.py
viralconseq/setup_cli.py
viralconseq/validators.py
viralconseq.egg-info/PKG-INFO
viralconseq.egg-info/SOURCES.txt
viralconseq.egg-info/dependency_links.txt
viralconseq.egg-info/entry_points.txt
viralconseq.egg-info/requires.txt
viralconseq.egg-info/top_level.txt
viralconseq/scripts/__init__.py
viralconseq/scripts/consensus_illumina.smk
viralconseq/scripts/consensus_illumina_segmented.smk
viralconseq/scripts/consensus_nanopore.smk
viralconseq/scripts/consensus_nanopore_segmented.smk
viralconseq/scripts/viralqc_setup.smk
viralconseq/scripts/envs/alignment.yaml
viralconseq/scripts/envs/clair3.yaml
viralconseq/scripts/envs/consensus.yaml
viralconseq/scripts/envs/qc.yaml
viralconseq/scripts/envs/utils.yaml
viralconseq/scripts/envs/viralqc.yaml
viralconseq/scripts/python/__init__.py
viralconseq/scripts/python/build_report.py
viralconseq/scripts/python/build_summary.py
viralconseq/scripts/python/calculate_assembly_stats.py
viralconseq/scripts/python/collect_benchmarks.py
viralconseq/scripts/python/collect_consensus.py
viralconseq/scripts/python/fetch_clair3_model.py
viralconseq/scripts/python/rename_sequences.py
viralconseq/scripts/python/tool_versions.py
viralconseq/scripts/rules/__init__.py
viralconseq/scripts/rules/alignment_illumina.smk
viralconseq/scripts/rules/alignment_nanopore.smk
viralconseq/scripts/rules/collect.smk
viralconseq/scripts/rules/common.smk
viralconseq/scripts/rules/consensus_illumina.smk
viralconseq/scripts/rules/consensus_illumina_common.smk
viralconseq/scripts/rules/consensus_nanopore.smk
viralconseq/scripts/rules/consensus_nanopore_common.smk
viralconseq/scripts/rules/provenance.smk
viralconseq/scripts/rules/qc_illumina.smk
viralconseq/scripts/rules/report.smk
viralconseq/scripts/rules/stats.smk
viralconseq/scripts/rules/viralqc.smk
viralconseq/scripts/templates/report.html