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ViroConstrictor/workflow/envs/Alignment.yaml
ViroConstrictor/workflow/envs/Clean.yaml
ViroConstrictor/workflow/envs/Consensus.yaml
ViroConstrictor/workflow/envs/ORF_analysis.yaml
ViroConstrictor/workflow/envs/core_scripts.yaml
ViroConstrictor/workflow/envs/mr_scripts.yaml
ViroConstrictor/workflow/helpers/__init__.py
ViroConstrictor/workflow/helpers/base_script_class.py
ViroConstrictor/workflow/helpers/containers.py
ViroConstrictor/workflow/helpers/directories.py
ViroConstrictor/workflow/helpers/generic_workflow_methods.py
ViroConstrictor/workflow/helpers/preset_aliases.json
ViroConstrictor/workflow/helpers/preset_params.json
ViroConstrictor/workflow/helpers/presets.py
ViroConstrictor/workflow/main/__init__.py
ViroConstrictor/workflow/main/components/clean.adapter_removal.smk
ViroConstrictor/workflow/main/components/clean.data_filter.smk
ViroConstrictor/workflow/main/components/clean.primer_removal.smk
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ViroConstrictor/workflow/main/components/preparation.primers.smk
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ViroConstrictor/workflow/main/components/results.sequences.smk
ViroConstrictor/workflow/main/components/stats.post_clean.smk
ViroConstrictor/workflow/main/components/stats.pre_clean.smk
ViroConstrictor/workflow/main/configs/multiqc.yaml
ViroConstrictor/workflow/main/scripts/__init__.py
ViroConstrictor/workflow/main/scripts/aggregate_combined_files.py
ViroConstrictor/workflow/main/scripts/amplicon_covs.py
ViroConstrictor/workflow/main/scripts/boc.py
ViroConstrictor/workflow/main/scripts/clipper.py
ViroConstrictor/workflow/main/scripts/combine_fasta.py
ViroConstrictor/workflow/main/scripts/combine_tabular.py
ViroConstrictor/workflow/main/scripts/concat_amplicon_covs.py
ViroConstrictor/workflow/main/scripts/extract_gff.py
ViroConstrictor/workflow/main/scripts/extract_sample_from_fasta.py
ViroConstrictor/workflow/main/scripts/fastqc.sh
ViroConstrictor/workflow/main/scripts/filter_bed_input.py
ViroConstrictor/workflow/main/scripts/group_aminoacids.py
ViroConstrictor/workflow/main/scripts/prepare_refs.py
ViroConstrictor/workflow/main/scripts/vcf_to_tsv.py
ViroConstrictor/workflow/main/workflow.smk
ViroConstrictor/workflow/match_ref/__init__.py
ViroConstrictor/workflow/match_ref/components/filter.features.smk
ViroConstrictor/workflow/match_ref/components/filter.primers.smk
ViroConstrictor/workflow/match_ref/components/preparation.references.smk
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ViroConstrictor/workflow/match_ref/components/selection.reference.smk
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ViroConstrictor/workflow/match_ref/scripts/count_mapped_reads.py
ViroConstrictor/workflow/match_ref/scripts/filter_bed.py
ViroConstrictor/workflow/match_ref/scripts/filter_best_matching_ref.py
ViroConstrictor/workflow/match_ref/scripts/filter_gff.py
ViroConstrictor/workflow/match_ref/scripts/filter_references.py
ViroConstrictor/workflow/match_ref/scripts/group_refs.py
ViroConstrictor/workflow/match_ref/workflow.smk
site-packages/ViroConstrictor/__init__.py
site-packages/ViroConstrictor/__main__.py
site-packages/ViroConstrictor/functions.py
site-packages/ViroConstrictor/genbank.py
site-packages/ViroConstrictor/logging.py
site-packages/ViroConstrictor/match_ref.py
site-packages/ViroConstrictor/parser.py
site-packages/ViroConstrictor/runreport.py
site-packages/ViroConstrictor/samplesheet.py
site-packages/ViroConstrictor/scheduler.py
site-packages/ViroConstrictor/update.py
site-packages/ViroConstrictor/userprofile.py
site-packages/ViroConstrictor/validatefasta.py
site-packages/ViroConstrictor/workflow/__init__.py
site-packages/ViroConstrictor/workflow/envs/Alignment.yaml
site-packages/ViroConstrictor/workflow/envs/Clean.yaml
site-packages/ViroConstrictor/workflow/envs/Consensus.yaml
site-packages/ViroConstrictor/workflow/envs/ORF_analysis.yaml
site-packages/ViroConstrictor/workflow/envs/core_scripts.yaml
site-packages/ViroConstrictor/workflow/envs/mr_scripts.yaml
site-packages/ViroConstrictor/workflow/helpers/__init__.py
site-packages/ViroConstrictor/workflow/helpers/base_script_class.py
site-packages/ViroConstrictor/workflow/helpers/containers.py
site-packages/ViroConstrictor/workflow/helpers/directories.py
site-packages/ViroConstrictor/workflow/helpers/generic_workflow_methods.py
site-packages/ViroConstrictor/workflow/helpers/preset_aliases.json
site-packages/ViroConstrictor/workflow/helpers/preset_params.json
site-packages/ViroConstrictor/workflow/helpers/presets.py
site-packages/ViroConstrictor/workflow/main/__init__.py
site-packages/ViroConstrictor/workflow/main/components/clean.adapter_removal.smk
site-packages/ViroConstrictor/workflow/main/components/clean.data_filter.smk
site-packages/ViroConstrictor/workflow/main/components/clean.primer_removal.smk
site-packages/ViroConstrictor/workflow/main/components/preparation.features.smk
site-packages/ViroConstrictor/workflow/main/components/preparation.primers.smk
site-packages/ViroConstrictor/workflow/main/components/preparation.references.smk
site-packages/ViroConstrictor/workflow/main/components/results.combined.smk
site-packages/ViroConstrictor/workflow/main/components/results.concatenations.smk
site-packages/ViroConstrictor/workflow/main/components/results.reporting_metrics.smk
site-packages/ViroConstrictor/workflow/main/components/results.sequences.smk
site-packages/ViroConstrictor/workflow/main/components/stats.post_clean.smk
site-packages/ViroConstrictor/workflow/main/components/stats.pre_clean.smk
site-packages/ViroConstrictor/workflow/main/configs/multiqc.yaml
site-packages/ViroConstrictor/workflow/main/scripts/__init__.py
site-packages/ViroConstrictor/workflow/main/scripts/aggregate_combined_files.py
site-packages/ViroConstrictor/workflow/main/scripts/amplicon_covs.py
site-packages/ViroConstrictor/workflow/main/scripts/boc.py
site-packages/ViroConstrictor/workflow/main/scripts/clipper.py
site-packages/ViroConstrictor/workflow/main/scripts/combine_fasta.py
site-packages/ViroConstrictor/workflow/main/scripts/combine_tabular.py
site-packages/ViroConstrictor/workflow/main/scripts/concat_amplicon_covs.py
site-packages/ViroConstrictor/workflow/main/scripts/extract_gff.py
site-packages/ViroConstrictor/workflow/main/scripts/extract_sample_from_fasta.py
site-packages/ViroConstrictor/workflow/main/scripts/fastqc.sh
site-packages/ViroConstrictor/workflow/main/scripts/filter_bed_input.py
site-packages/ViroConstrictor/workflow/main/scripts/group_aminoacids.py
site-packages/ViroConstrictor/workflow/main/scripts/prepare_refs.py
site-packages/ViroConstrictor/workflow/main/scripts/vcf_to_tsv.py
site-packages/ViroConstrictor/workflow/main/workflow.smk
site-packages/ViroConstrictor/workflow/match_ref/__init__.py
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site-packages/ViroConstrictor/workflow/match_ref/components/filter.primers.smk
site-packages/ViroConstrictor/workflow/match_ref/components/preparation.references.smk
site-packages/ViroConstrictor/workflow/match_ref/components/selection.alignment.smk
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site-packages/ViroConstrictor/workflow/match_ref/scripts/__init__.py
site-packages/ViroConstrictor/workflow/match_ref/scripts/count_mapped_reads.py
site-packages/ViroConstrictor/workflow/match_ref/scripts/filter_bed.py
site-packages/ViroConstrictor/workflow/match_ref/scripts/filter_best_matching_ref.py
site-packages/ViroConstrictor/workflow/match_ref/scripts/filter_gff.py
site-packages/ViroConstrictor/workflow/match_ref/scripts/filter_references.py
site-packages/ViroConstrictor/workflow/match_ref/scripts/group_refs.py
site-packages/ViroConstrictor/workflow/match_ref/workflow.smk
site-packages/ViroConstrictor/workflow_config.py
site-packages/ViroConstrictor/workflow_executor.py
site-packages/snakemake_logger_plugin_viroconstrictor/__init__.py
site-packages/snakemake_logger_plugin_viroconstrictor/handler.py
site-packages/viroconstrictor-1.6.6.dist-info/INSTALLER
site-packages/viroconstrictor-1.6.6.dist-info/METADATA
site-packages/viroconstrictor-1.6.6.dist-info/RECORD
site-packages/viroconstrictor-1.6.6.dist-info/REQUESTED
site-packages/viroconstrictor-1.6.6.dist-info/WHEEL
site-packages/viroconstrictor-1.6.6.dist-info/direct_url.json
site-packages/viroconstrictor-1.6.6.dist-info/entry_points.txt
site-packages/viroconstrictor-1.6.6.dist-info/licenses/LICENSE
snakemake_logger_plugin_viroconstrictor/__init__.py
snakemake_logger_plugin_viroconstrictor/handler.py
