LICENSE
MANIFEST.in
README.md
pyproject.toml
METACARP.egg-info/PKG-INFO
METACARP.egg-info/SOURCES.txt
METACARP.egg-info/dependency_links.txt
METACARP.egg-info/entry_points.txt
METACARP.egg-info/requires.txt
METACARP.egg-info/top_level.txt
metacarp/__init__.py
metacarp/galaxy.py
metacarp/run_GMM_screening.py
metacarp/run_metacarp.py
metacarp/version.py
metacarp/app/__init__.py
metacarp/app/command.py
metacarp/app/utils/__init__.py
metacarp/app/utils/loggingutils.py
metacarp/app/utils/reportutils.py
metacarp/app/utils/snakemakeutils.py
metacarp/app/utils/workflowutils.py
metacarp/camel_gene_detection/__init__.py
metacarp/camel_gene_detection/app/__init__.py
metacarp/camel_gene_detection/app/camel.py
metacarp/camel_gene_detection/app/command/__init__.py
metacarp/camel_gene_detection/app/command/command.py
metacarp/camel_gene_detection/app/components/__init__.py
metacarp/camel_gene_detection/app/components/filesystemhelper.py
metacarp/camel_gene_detection/app/components/mainscriptutils.py
metacarp/camel_gene_detection/app/components/statisticsutils.py
metacarp/camel_gene_detection/app/components/blast/__init__.py
metacarp/camel_gene_detection/app/components/blast/blasthitstatistics.py
metacarp/camel_gene_detection/app/components/files/__init__.py
metacarp/camel_gene_detection/app/components/files/fastqutils.py
metacarp/camel_gene_detection/app/components/files/fileutils.py
metacarp/camel_gene_detection/app/components/galaxy/__init__.py
metacarp/camel_gene_detection/app/components/galaxy/galaxyutils.py
metacarp/camel_gene_detection/app/components/genedetection/__init__.py
metacarp/camel_gene_detection/app/components/genedetection/genedetectionblasthit.py
metacarp/camel_gene_detection/app/components/genedetection/genedetectionhitbase.py
metacarp/camel_gene_detection/app/components/genedetection/genedetectionkmahit.py
metacarp/camel_gene_detection/app/components/genedetection/genedetectionsrst2hit.py
metacarp/camel_gene_detection/app/components/genedetection/genedetectionutils.py
metacarp/camel_gene_detection/app/components/genedetection/mapping.py
metacarp/camel_gene_detection/app/components/genedetection/mappingjson.py
metacarp/camel_gene_detection/app/components/html/__init__.py
metacarp/camel_gene_detection/app/components/html/htmlbase.py
metacarp/camel_gene_detection/app/components/html/htmlcitation.py
metacarp/camel_gene_detection/app/components/html/htmlelement.py
metacarp/camel_gene_detection/app/components/html/htmlexpandablediv.py
metacarp/camel_gene_detection/app/components/html/htmlexpandabletable.py
metacarp/camel_gene_detection/app/components/html/htmlreport.py
metacarp/camel_gene_detection/app/components/html/htmlreportsection.py
metacarp/camel_gene_detection/app/components/html/htmltablecell.py
metacarp/camel_gene_detection/app/components/html/htmltableformatter.py
metacarp/camel_gene_detection/app/components/workflows/__init__.py
metacarp/camel_gene_detection/app/components/workflows/genedetectionwrapper.py
metacarp/camel_gene_detection/app/components/workflows/trimmingilluminawrapper.py
metacarp/camel_gene_detection/app/components/workflows/trimmingontwrapper.py
metacarp/camel_gene_detection/app/components/workflows/workflowutils.py
metacarp/camel_gene_detection/app/components/workflows/readtype/__init__.py
metacarp/camel_gene_detection/app/components/workflows/readtype/basereadtypehelper.py
metacarp/camel_gene_detection/app/components/workflows/readtype/illuminahelper.py
metacarp/camel_gene_detection/app/components/workflows/readtype/onthelper.py
metacarp/camel_gene_detection/app/components/workflows/utils/__init__.py
metacarp/camel_gene_detection/app/components/workflows/utils/fastqinput.py
metacarp/camel_gene_detection/app/error/__init__.py
metacarp/camel_gene_detection/app/error/invalidinputerror.py
metacarp/camel_gene_detection/app/error/invalidinputspecificationerror.py
metacarp/camel_gene_detection/app/error/invalidparametererror.py
metacarp/camel_gene_detection/app/error/pipelineexecutionerror.py
metacarp/camel_gene_detection/app/error/snakemakeexecutionerror.py
metacarp/camel_gene_detection/app/error/toolexecutionerror.py
metacarp/camel_gene_detection/app/io/__init__.py
metacarp/camel_gene_detection/app/io/toolio.py
metacarp/camel_gene_detection/app/io/tooliodirectory.py
metacarp/camel_gene_detection/app/io/tooliofile.py
metacarp/camel_gene_detection/app/io/tooliovalue.py
metacarp/camel_gene_detection/app/loggers/__init__.py
metacarp/camel_gene_detection/app/loggers/fileloggerutils.py
metacarp/camel_gene_detection/app/parameter/__init__.py
metacarp/camel_gene_detection/app/parameter/parameter.py
metacarp/camel_gene_detection/app/pipeline/__init__.py
metacarp/camel_gene_detection/app/pipeline/pipeline.py
metacarp/camel_gene_detection/app/pipeline/step.py
metacarp/camel_gene_detection/app/services/__init__.py
metacarp/camel_gene_detection/app/services/basetoolservice.py
metacarp/camel_gene_detection/app/services/yamltoolservice.py
metacarp/camel_gene_detection/app/snakemake/__init__.py
metacarp/camel_gene_detection/app/snakemake/snakemakeutils.py
metacarp/camel_gene_detection/app/snakemake/snakepipelineutils.py
metacarp/camel_gene_detection/app/tools/__init__.py
metacarp/camel_gene_detection/app/tools/tool.py
metacarp/camel_gene_detection/app/tools/toolpipeable.py
metacarp/camel_gene_detection/app/tools/kma/__init__.py
metacarp/camel_gene_detection/app/tools/kma/kma.py
metacarp/camel_gene_detection/app/tools/kma/kma.yml
metacarp/camel_gene_detection/app/tools/kma/kmagenedetectionhitextractor.py
metacarp/camel_gene_detection/app/tools/kma/kmagenedetectionhitextractor.yml
metacarp/camel_gene_detection/app/tools/kma/kmatypinghitextractor.py
metacarp/camel_gene_detection/app/tools/kma/kmatypinghitextractor.yml
metacarp/camel_gene_detection/app/tools/pipelines/__init__.py
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/__init__.py
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/alignmentextractor.py
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/alignmentextractor.yml
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/blasthitfiltering.py
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/blasthitfiltering.yml
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/dbmanager.py
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/dbmanager.yml
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/htmlreportergenedetection.py
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/htmlreportergenedetection.yml
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/srst2hitextractor.py
metacarp/camel_gene_detection/app/tools/pipelines/genedetection/srst2hitextractor.yml
metacarp/camel_gene_detection/config/__init__.py
metacarp/camel_gene_detection/config/main.yml
metacarp/camel_gene_detection/resources/__init__.py
metacarp/camel_gene_detection/resources/css/style.css
metacarp/camel_gene_detection/resources/fonts/FreeSans.ttf
metacarp/camel_gene_detection/resources/fonts/FreeSansBold.ttf
metacarp/camel_gene_detection/resources/javascript/__init__.py
metacarp/camel_gene_detection/resources/javascript/jquery-3.2.1.min.js
metacarp/camel_gene_detection/resources/snakefile/__init__.py
metacarp/camel_gene_detection/resources/snakefile/gene_detection.py
metacarp/camel_gene_detection/resources/snakefile/gene_detection.smk
metacarp/camel_gene_detection/resources/snakefile/gene_detection_blast.smk
metacarp/camel_gene_detection/resources/snakefile/gene_detection_kma.smk
metacarp/camel_gene_detection/resources/snakefile/gene_detection_srst2.smk
metacarp/camel_gene_detection/resources/snakefile/read_simulation.py
metacarp/camel_gene_detection/resources/snakefile/read_simulation.smk
metacarp/camel_gene_detection/resources/snakefile/trimming.py
metacarp/camel_gene_detection/resources/snakefile/trimming_illumina.py
metacarp/camel_gene_detection/resources/snakefile/trimming_illumina.smk
metacarp/camel_gene_detection/resources/snakefile/trimming_ont.py
metacarp/camel_gene_detection/resources/snakefile/trimming_ont.smk
metacarp/camel_gene_detection/resources/static/logo-sciensano.png
metacarp/camel_gene_detection/scripts/__init__.py
metacarp/camel_gene_detection/scripts/genedetection/__init__.py
metacarp/camel_gene_detection/scripts/genedetection/maingenedetection.py
metacarp/resources/__init__.py
metacarp/resources/allergens.tsv
metacarp/resources/confidence_cutoffs.json
metacarp/resources/style.css
metacarp/resources/usual_suspects.tsv
metacarp/resources/DB_GMM/V6/genes-vectors/db_metadata.txt
metacarp/resources/DB_GMM/V6/genes-vectors/genes-vectors-clustered_80.fasta
metacarp/resources/DB_GMM/V6/genes-vectors/genes-vectors.fasta
metacarp/resources/DB_GMM/V6/genes-vectors/mapping_full.json
metacarp/resources/DB_GMM/V6/junctions/GMM_junctions-clustered_80.fasta
metacarp/resources/DB_GMM/V6/junctions/db_metadata.txt
metacarp/resources/DB_GMM/V6/junctions/gmm_junctions.fasta
metacarp/resources/DB_GMM/V6/junctions/mapping_full.json
metacarp/resources/citations/Orval_2025-vitamins.json
metacarp/resources/snakefiles/GMM_screening.smk
metacarp/resources/snakefiles/__init__.py
metacarp/resources/snakefiles/ilmn_rules.smk
metacarp/resources/snakefiles/main_workflow.smk
metacarp/resources/snakefiles/ont_rules.smk