MANIFEST.in
README.md
setup.py
staphb_toolkit/__init__.py
staphb_toolkit/toolkit_apps.py
staphb_toolkit/toolkit_workflows.py
staphb_toolkit.egg-info/PKG-INFO
staphb_toolkit.egg-info/SOURCES.txt
staphb_toolkit.egg-info/dependency_links.txt
staphb_toolkit.egg-info/entry_points.txt
staphb_toolkit.egg-info/requires.txt
staphb_toolkit.egg-info/top_level.txt
staphb_toolkit/apps/__init__.py
staphb_toolkit/apps/sb_mash_species.py
staphb_toolkit/core/__init__.py
staphb_toolkit/core/autopath.py
staphb_toolkit/core/basemount.py
staphb_toolkit/core/calldocker.py
staphb_toolkit/core/callsing.py
staphb_toolkit/core/docker_config.json
staphb_toolkit/core/fileparser.py
staphb_toolkit/core/sb_programs.py
staphb_toolkit/core/update_app.py
staphb_toolkit/lib/nextflow
staphb_toolkit/workflows/__init__.py
staphb_toolkit/workflows/universal_config_template.config
staphb_toolkit/workflows/cutshaw/cutshaw.config
staphb_toolkit/workflows/cutshaw/cutshaw.nf
staphb_toolkit/workflows/cutshaw/nextflow.config
staphb_toolkit/workflows/cutshaw/configs/cutshaw_config_template.config
staphb_toolkit/workflows/cutshaw/configs/docker.config
staphb_toolkit/workflows/cutshaw/configs/docker_containers.config
staphb_toolkit/workflows/cutshaw/configs/singularity.config
staphb_toolkit/workflows/cutshaw/pt_genomes/LMP18-H2446.fasta
staphb_toolkit/workflows/cutshaw/pt_genomes/LMP18-H8393.fasta
staphb_toolkit/workflows/cutshaw/pt_genomes/SAP18-0432.fasta
staphb_toolkit/workflows/cutshaw/pt_genomes/SAP18-6199.fasta
staphb_toolkit/workflows/cutshaw/pt_genomes/SAP18-8729.fasta
staphb_toolkit/workflows/cutshaw/pt_genomes/SAP18-H9654.fasta
staphb_toolkit/workflows/cutshaw/pt_genomes/reference_list.txt
staphb_toolkit/workflows/dryad/dryad.config
staphb_toolkit/workflows/dryad/dryad.nf
staphb_toolkit/workflows/dryad/dryad.py
staphb_toolkit/workflows/dryad/dryad_report.py
staphb_toolkit/workflows/dryad/nextflow.config
staphb_toolkit/workflows/dryad/rebuild_report.nf
staphb_toolkit/workflows/dryad/assets/dryad_logo_250.png
staphb_toolkit/workflows/dryad/assets/dryad_logo_500.png
staphb_toolkit/workflows/dryad/configs/docker.config
staphb_toolkit/workflows/dryad/configs/docker_containers.config
staphb_toolkit/workflows/dryad/configs/dryad_config_template.config
staphb_toolkit/workflows/dryad/configs/multiqc_config.yaml
staphb_toolkit/workflows/dryad/configs/singularity.config
staphb_toolkit/workflows/dryad/report/report.Rmd
staphb_toolkit/workflows/foushee/foushee.config
staphb_toolkit/workflows/foushee/foushee.nf
staphb_toolkit/workflows/foushee/nextflow.config
staphb_toolkit/workflows/foushee/configs/aws_batch.config
staphb_toolkit/workflows/foushee/configs/docker.config
staphb_toolkit/workflows/foushee/configs/docker_containers.config
staphb_toolkit/workflows/foushee/configs/foushee_config_template.config
staphb_toolkit/workflows/foushee/configs/singularity.config
staphb_toolkit/workflows/foushee/report/report.Rmd
staphb_toolkit/workflows/hickory/hickory.config
staphb_toolkit/workflows/hickory/hickory.nf
staphb_toolkit/workflows/hickory/nextflow.config
staphb_toolkit/workflows/hickory/configs/aws_batch.config
staphb_toolkit/workflows/hickory/configs/docker.config
staphb_toolkit/workflows/hickory/configs/docker_containers.config
staphb_toolkit/workflows/hickory/configs/hickory_config_template.config
staphb_toolkit/workflows/hickory/configs/singularity.config
staphb_toolkit/workflows/monroe/monroe.config
staphb_toolkit/workflows/monroe/monroe_cluster_analysis.nf
staphb_toolkit/workflows/monroe/monroe_ont_assembly.nf
staphb_toolkit/workflows/monroe/monroe_pe_assembly.nf
staphb_toolkit/workflows/monroe/nextflow.config
staphb_toolkit/workflows/monroe/configs/cluster_user_config.config
staphb_toolkit/workflows/monroe/configs/docker.config
staphb_toolkit/workflows/monroe/configs/docker_containers.config
staphb_toolkit/workflows/monroe/configs/ont_user_config.config
staphb_toolkit/workflows/monroe/configs/pe_user_config.config
staphb_toolkit/workflows/monroe/configs/singularity.config
staphb_toolkit/workflows/monroe/report/report.Rmd
staphb_toolkit/workflows/tredegar/nextflow.config
staphb_toolkit/workflows/tredegar/tredegar.config
staphb_toolkit/workflows/tredegar/tredegar.nf
staphb_toolkit/workflows/tredegar/configs/aws_batch.config
staphb_toolkit/workflows/tredegar/configs/docker.config
staphb_toolkit/workflows/tredegar/configs/docker_containers.config
staphb_toolkit/workflows/tredegar/configs/singularity.config
staphb_toolkit/workflows/tredegar/configs/tredegar_config_template.config