LICENSE.txt
MANIFEST.in
README.md
setup.cfg
setup.py
bohra/CustomLog.py
bohra/SnpDetection.py
bohra/Utils.py
bohra/__init__.py
bohra/bohra.py
bohra/bohra_install.sh
bohra/main.nf
bohra/nextflow.config
bohra/version.py
bohra.egg-info/PKG-INFO
bohra.egg-info/SOURCES.txt
bohra.egg-info/dependency_links.txt
bohra.egg-info/entry_points.txt
bohra.egg-info/not-zip-safe
bohra.egg-info/requires.txt
bohra.egg-info/top_level.txt
bohra/modules/collation/functions.nf
bohra/modules/collation/main.nf
bohra/modules/collation/bin/add_header_mlst.py
bohra/modules/collation/bin/collate_asm.py
bohra/modules/collation/bin/collate_kraken2.py
bohra/modules/collation/bin/collate_stats.py
bohra/modules/collation/bin/collate_tables.py
bohra/modules/collation/bin/compile.py
bohra/modules/collation/bin/snippy_qc.py
bohra/modules/collation/bin/wrangle_mobsuite.py
bohra/modules/csvtk/functions.nf
bohra/modules/csvtk/main.nf
bohra/modules/csvtk/meta.yml
bohra/modules/ectyper/functions.nf
bohra/modules/ectyper/main.nf
bohra/modules/ectyper/meta.yml
bohra/modules/emmtyper/functions.nf
bohra/modules/emmtyper/main.nf
bohra/modules/emmtyper/meta.yml
bohra/modules/gubbins/functions.nf
bohra/modules/gubbins/main.nf
bohra/modules/gubbins/meta.yml
bohra/modules/iqtree/functions.nf
bohra/modules/iqtree/main.nf
bohra/modules/iqtree/meta.yml
bohra/modules/kleborate/functions.nf
bohra/modules/kleborate/main.nf
bohra/modules/kleborate/meta.yml
bohra/modules/kmc/functions.nf
bohra/modules/kmc/main.nf
bohra/modules/kmc/meta.yml
bohra/modules/kraken2/functions.nf
bohra/modules/kraken2/main.nf
bohra/modules/kraken2/meta.yml
bohra/modules/lissero/functions.nf
bohra/modules/lissero/main.nf
bohra/modules/lissero/meta.yml
bohra/modules/mash/sketch/functions.nf
bohra/modules/mash/sketch/main.nf
bohra/modules/mash/sketch/meta.yml
bohra/modules/mash/triangle/functions.nf
bohra/modules/mash/triangle/main.nf
bohra/modules/mash/triangle/meta.yml
bohra/modules/meningotype/functions.nf
bohra/modules/meningotype/main.nf
bohra/modules/meningotype/meta.yml
bohra/modules/mlst/functions.nf
bohra/modules/mlst/main.nf
bohra/modules/mlst/meta.yml
bohra/modules/mobsuite/functions.nf
bohra/modules/mobsuite/main.nf
bohra/modules/mobsuite/meta.yml
bohra/modules/ngmaster/functions.nf
bohra/modules/ngmaster/main.nf
bohra/modules/ngmaster/meta.yml
bohra/modules/panaroo/functions.nf
bohra/modules/panaroo/main.nf
bohra/modules/panaroo/meta.yml
bohra/modules/prokka/functions.nf
bohra/modules/prokka/main.nf
bohra/modules/prokka/meta.yml
bohra/modules/quicktree/functions.nf
bohra/modules/quicktree/main.nf
bohra/modules/quicktree/meta.yml
bohra/modules/resistome/functions.nf
bohra/modules/resistome/main.nf
bohra/modules/resistome/meta.yml
bohra/modules/resistome/bin/combine.py
bohra/modules/resistome/bin/concat.py
bohra/modules/resistome/bin/meta.yaml
bohra/modules/roary2svg/functions.nf
bohra/modules/roary2svg/main.nf
bohra/modules/roary2svg/meta.yml
bohra/modules/roary2svg/bin/roary2svg.pl
bohra/modules/seqkit/fx2tab/functions.nf
bohra/modules/seqkit/fx2tab/main.nf
bohra/modules/seqkit/fx2tab/meta.yml
bohra/modules/seqkit/stats/functions.nf
bohra/modules/seqkit/stats/main.nf
bohra/modules/seqkit/stats/meta.yml
bohra/modules/seqtk/functions.nf
bohra/modules/seqtk/main.nf
bohra/modules/seqtk/meta.yml
bohra/modules/shovill/functions.nf
bohra/modules/shovill/main.nf
bohra/modules/shovill/meta.yml
bohra/modules/skesa/functions.nf
bohra/modules/skesa/main.nf
bohra/modules/skesa/meta.yml
bohra/modules/snippy/functions.nf
bohra/modules/snippy/main.nf
bohra/modules/snippy/meta.yml
bohra/modules/snippy_clean/functions.nf
bohra/modules/snippy_clean/main.nf
bohra/modules/snippy_clean/meta.yml
bohra/modules/snippy_core/functions.nf
bohra/modules/snippy_core/main.nf
bohra/modules/snippy_core/meta.yml
bohra/modules/snp_dists/functions.nf
bohra/modules/snp_dists/main.nf
bohra/modules/snp_dists/meta.yml
bohra/modules/spades/functions.nf
bohra/modules/spades/main.nf
bohra/modules/spades/meta.yml
bohra/modules/stype/functions.nf
bohra/modules/stype/main.nf
bohra/modules/stype/meta.yml
bohra/modules/utils/functions.nf
bohra/modules/utils/main.nf
bohra/modules/utils/meta.yml
bohra/modules/utils/bin/extract_species.py
bohra/templates/cluster.tmpl
bohra/templates/config_snippy.yaml
bohra/templates/index.html
bohra/templates/report_analysis.json
bohra/templates/typers.json
bohra/workflows/assemble.nf
bohra/workflows/collation.nf
bohra/workflows/default.nf
bohra/workflows/pangenome.nf
bohra/workflows/preview.nf
bohra/workflows/read_assessment.nf
bohra/workflows/snps.nf
bohra/workflows/species.nf
bohra/workflows/typing.nf
bohra/workflows/versions.nf
tests/test_bohra.py