README.md
setup.py
assemblerflow/__init__.py
assemblerflow/assemblerflow.py
assemblerflow/nextflow.config
assemblerflow/profiles.config
assemblerflow.egg-info/PKG-INFO
assemblerflow.egg-info/SOURCES.txt
assemblerflow.egg-info/dependency_links.txt
assemblerflow.egg-info/entry_points.txt
assemblerflow.egg-info/requires.txt
assemblerflow.egg-info/top_level.txt
assemblerflow/bin/final_POST.sh
assemblerflow/bin/merge_json.py
assemblerflow/bin/parse_true_coverage.py
assemblerflow/bin/prepare_reports.py
assemblerflow/bin/report_POST.sh
assemblerflow/bin/set_dotfiles.sh
assemblerflow/bin/startup_POST.sh
assemblerflow/generator/__init__.py
assemblerflow/generator/engine.py
assemblerflow/generator/error_handling.py
assemblerflow/generator/footer_skeleton.py
assemblerflow/generator/header_skeleton.py
assemblerflow/generator/pipeline_parser.py
assemblerflow/generator/process.py
assemblerflow/generator/process_details.py
assemblerflow/generator/recipe.py
assemblerflow/generator/components/__init__.py
assemblerflow/generator/components/annotation.py
assemblerflow/generator/components/assembly.py
assemblerflow/generator/components/assembly_processing.py
assemblerflow/generator/components/distance_estimation.py
assemblerflow/generator/components/downloads.py
assemblerflow/generator/components/mapping.py
assemblerflow/generator/components/mlst.py
assemblerflow/generator/components/reads_quality_control.py
assemblerflow/generator/components/typing.py
assemblerflow/generator/templates/Helper.groovy
assemblerflow/generator/templates/abricate.nf
assemblerflow/generator/templates/assembly_mapping.nf
assemblerflow/generator/templates/check_coverage.nf
assemblerflow/generator/templates/chewbbaca.nf
assemblerflow/generator/templates/compiler_channels.txt
assemblerflow/generator/templates/containers.config
assemblerflow/generator/templates/fastqc.nf
assemblerflow/generator/templates/fastqc_trimmomatic.nf
assemblerflow/generator/templates/init.nf
assemblerflow/generator/templates/integrity_coverage.nf
assemblerflow/generator/templates/mapping_patlas.nf
assemblerflow/generator/templates/mash_dist.nf
assemblerflow/generator/templates/mash_screen.nf
assemblerflow/generator/templates/mlst.nf
assemblerflow/generator/templates/params.config
assemblerflow/generator/templates/patho_typing.nf
assemblerflow/generator/templates/patlas_consensus.nf
assemblerflow/generator/templates/pilon.nf
assemblerflow/generator/templates/pipeline_graph.html
assemblerflow/generator/templates/post.txt
assemblerflow/generator/templates/process_skesa.nf
assemblerflow/generator/templates/process_spades.nf
assemblerflow/generator/templates/prokka.nf
assemblerflow/generator/templates/reads_download.nf
assemblerflow/generator/templates/report_compiler.nf
assemblerflow/generator/templates/report_post.txt
assemblerflow/generator/templates/resources.config
assemblerflow/generator/templates/seq_typing.nf
assemblerflow/generator/templates/skesa.nf
assemblerflow/generator/templates/spades.nf
assemblerflow/generator/templates/status_compiler.nf
assemblerflow/generator/templates/trace_compiler.nf
assemblerflow/generator/templates/trimmomatic.nf
assemblerflow/generator/templates/true_coverage.nf
assemblerflow/generator/templates/user.config
assemblerflow/lib/CheckParams.groovy
assemblerflow/templates/__init__.py
assemblerflow/templates/assembly_report.py
assemblerflow/templates/fastqc.py
assemblerflow/templates/fastqc_report.py
assemblerflow/templates/integrity_coverage.py
assemblerflow/templates/mapping2json.py
assemblerflow/templates/mashdist2json.py
assemblerflow/templates/mashscreen2json.py
assemblerflow/templates/pATLAS_consensus_json.py
assemblerflow/templates/pipeline_status.py
assemblerflow/templates/process_abricate.py
assemblerflow/templates/process_assembly.py
assemblerflow/templates/process_assembly_mapping.py
assemblerflow/templates/skesa.py
assemblerflow/templates/spades.py
assemblerflow/templates/trimmomatic.py
assemblerflow/templates/trimmomatic_report.py