├── .gitignore ├── .gitmodules ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── changelog.md ├── docker └── Dockerfile ├── docs ├── Makefile ├── _static │ └── custom.css ├── about │ └── about.rst ├── conf.py ├── dev │ ├── containers.rst │ ├── create_process.rst │ ├── create_recipe.rst │ ├── create_recipes.rst │ ├── create_template.rst │ ├── general_orientation.rst │ ├── pipeline_reporting.rst │ ├── process_dotfiles.rst │ └── reports.rst ├── flowcraft.flowcraft.rst ├── flowcraft.generator.components.annotation.rst ├── flowcraft.generator.components.assembly.rst ├── flowcraft.generator.components.assembly_processing.rst ├── flowcraft.generator.components.distance_estimation.rst ├── flowcraft.generator.components.downloads.rst ├── flowcraft.generator.components.metagenomics.rst ├── flowcraft.generator.components.mlst.rst ├── flowcraft.generator.components.patlas_mapping.rst ├── flowcraft.generator.components.reads_quality_control.rst ├── flowcraft.generator.components.rst ├── flowcraft.generator.components.typing.rst ├── flowcraft.generator.engine.rst ├── flowcraft.generator.error_handling.rst ├── flowcraft.generator.footer_skeleton.rst ├── flowcraft.generator.header_skeleton.rst ├── flowcraft.generator.inspect.rst ├── flowcraft.generator.pipeline_parser.rst ├── flowcraft.generator.process.rst ├── flowcraft.generator.process_details.rst ├── flowcraft.generator.recipe.rst ├── flowcraft.generator.rst ├── flowcraft.rst ├── flowcraft.templates.assembly_report.rst ├── flowcraft.templates.fastqc.rst ├── flowcraft.templates.fastqc_report.rst ├── flowcraft.templates.flowcraft_utils.flowcraft_base.rst ├── flowcraft.templates.flowcraft_utils.rst ├── flowcraft.templates.integrity_coverage.rst ├── flowcraft.templates.mapping2json.rst ├── flowcraft.templates.mashdist2json.rst ├── flowcraft.templates.mashscreen2json.rst ├── flowcraft.templates.megahit.rst ├── flowcraft.templates.metaspades.rst ├── flowcraft.templates.pATLAS_consensus_json.rst ├── flowcraft.templates.pipeline_status.rst ├── flowcraft.templates.process_abricate.rst ├── flowcraft.templates.process_assembly.rst ├── flowcraft.templates.process_assembly_mapping.rst ├── flowcraft.templates.rst ├── flowcraft.templates.skesa.rst ├── flowcraft.templates.spades.rst ├── flowcraft.templates.trimmomatic.rst ├── flowcraft.templates.trimmomatic_report.rst ├── flowcraft.tests.data_pipelines.rst ├── flowcraft.tests.rst ├── flowcraft.tests.test_assemblerflow.rst ├── flowcraft.tests.test_engine.rst ├── flowcraft.tests.test_pipeline_parser.rst ├── flowcraft.tests.test_process_details.rst ├── flowcraft.tests.test_processes.rst ├── flowcraft.tests.test_sanity.rst ├── getting_started │ ├── installation.rst │ └── overview.rst ├── index.rst ├── make.bat ├── resources │ ├── example_1.png │ ├── example_2.png │ ├── example_3.png │ ├── flowcraft_inspect_broadcast.png │ ├── flowcraft_inspect_terminal.png │ ├── flowcraft_report.png │ ├── flowcraft_report_watch.png │ ├── fork_1.png │ ├── fork_2.png │ ├── fork_3.png │ ├── fork_4.png │ ├── logo.png │ ├── logo_background.png │ ├── logo_large.png │ ├── logo_white.png │ └── reports │ │ ├── abricate_table.png │ │ ├── assembly_table_skesa.png │ │ ├── assembly_table_spades.png │ │ ├── assembly_table_viral_assembly.png │ │ ├── binning.png │ │ ├── chewbbaca_table.png │ │ ├── contig_size_distribution.png │ │ ├── fastqc_base_gc_content.png │ │ ├── fastqc_base_sequence_quality.png │ │ ├── fastqc_missing_data.png │ │ ├── fastqc_per_base_sequence_quality.png │ │ ├── fastqc_sequence_length.png │ │ ├── mash_dist_table.png │ │ ├── phylogenetic_tree.png │ │ ├── quality_control_table.png │ │ ├── read_mapping_remove_host.png │ │ ├── sliding_window_amr.png │ │ ├── sliding_window_mash_dist.png │ │ ├── sparkline.png │ │ ├── typing_table.png │ │ └── typing_table_dengue.png ├── setup.rst └── user │ ├── available_components.rst │ ├── basic_usage.rst │ ├── components │ ├── abricate.rst │ ├── assembly_mapping.rst │ ├── bowtie.rst │ ├── card_rgi.rst │ ├── check_coverage.rst │ ├── chewbbaca.rst │ ├── diamond.rst │ ├── downsample_fastq.rst │ ├── fast_ani.rst │ ├── fasterq_dump.rst │ ├── fastqc.rst │ ├── fastqc_trimmomatic.rst │ ├── filter_poly.rst │ ├── integrity_coverage.rst │ ├── kraken.rst │ ├── kraken2.rst │ ├── mapping_patlas.rst │ ├── mash_dist.rst │ ├── mash_screen.rst │ ├── mash_sketch_fasta.rst │ ├── mash_sketch_fastq.rst │ ├── maxbin2.rst │ ├── megahit.rst │ ├── metamlst.rst │ ├── metaspades.rst │ ├── midas_species.rst │ ├── mlst.rst │ ├── momps.rst │ ├── patho_typing.rst │ ├── pilon.rst │ ├── process_skesa.rst │ ├── process_spades.rst │ ├── prokka.rst │ ├── reads_download.rst │ ├── remove_host.rst │ ├── retrieve_mapped.rst │ ├── seq_typing.rst │ ├── sistr.rst │ ├── skesa.rst │ ├── spades.rst │ └── trimmomatic.rst │ ├── pipeline_building.rst │ ├── pipeline_configuration.rst │ ├── pipeline_inspect.rst │ ├── pipeline_reports.rst │ └── reports │ ├── abricate.rst │ ├── assembly_mapping.rst │ ├── check_coverage.rst │ ├── chewbbaca.rst │ ├── dengue_typing.rst │ ├── fastqc.rst │ ├── fastqc_trimmomatic.rst │ ├── integrity_coverage.rst │ ├── mash_dist.rst │ ├── maxbin2.rst │ ├── mlst.rst │ ├── patho_typing.rst │ ├── pilon.rst │ ├── process_mapping.rst │ ├── process_newick.rst │ ├── process_skesa.rst │ ├── process_spades.rst │ ├── process_viral_assembly.rst │ ├── seq_typing.rst │ ├── sistr.rst │ ├── trimmomatic.rst │ └── true_coverage.rst ├── flowcraft ├── __init__.py ├── bin │ ├── final_POST.sh │ ├── merge_json.py │ ├── metadata_POST.sh │ ├── parse_fasta.py │ ├── parse_true_coverage.py │ ├── prepare_reports.py │ ├── renamePE_samtoolsFASTQ.py │ ├── report_POST.sh │ ├── set_dotfiles.sh │ └── startup_POST.sh ├── flowcraft.py ├── generator │ ├── __init__.py │ ├── components │ │ ├── __init__.py │ │ ├── alignment.py │ │ ├── annotation.py │ │ ├── assembly.py │ │ ├── assembly_processing.py │ │ ├── distance_estimation.py │ │ ├── downloads.py │ │ ├── mapping.py │ │ ├── metagenomics.py │ │ ├── mlst.py │ │ ├── patlas_mapping.py │ │ ├── phylogeny.py │ │ ├── reads_quality_control.py │ │ ├── typing.py │ │ └── variant_calling.py │ ├── engine.py │ ├── error_handling.py │ ├── footer_skeleton.py │ ├── header_skeleton.py │ ├── inspect.py │ ├── pipeline_parser.py │ ├── process.py │ ├── process_collector.py │ ├── process_details.py │ ├── recipe.py │ ├── recipes │ │ ├── __init__.py │ │ ├── denim.py │ │ ├── innuca.py │ │ └── plasmids.py │ ├── report.py │ ├── templates │ │ ├── Helper.groovy │ │ ├── abricate.nf │ │ ├── abyss.nf │ │ ├── assembly_mapping.nf │ │ ├── bandage.nf │ │ ├── base_recalibrator.nf │ │ ├── bcalm.nf │ │ ├── bowtie.nf │ │ ├── bwa.nf │ │ ├── card_rgi.nf │ │ ├── check_coverage.nf │ │ ├── chewbbaca.nf │ │ ├── compiler_channels.txt │ │ ├── concoct.nf │ │ ├── containers.config │ │ ├── dengue_typing.nf │ │ ├── diamond.nf │ │ ├── downsample_fastq.nf │ │ ├── fast_ani.nf │ │ ├── fasterq_dump.nf │ │ ├── fastqc.nf │ │ ├── fastqc_trimmomatic.nf │ │ ├── filter_poly.nf │ │ ├── haplotypecaller.nf │ │ ├── init.nf │ │ ├── integrity_coverage.nf │ │ ├── kraken.nf │ │ ├── kraken2.nf │ │ ├── mafft.nf │ │ ├── mapping_patlas.nf │ │ ├── mark_duplicates.nf │ │ ├── mash_dist.nf │ │ ├── mash_screen.nf │ │ ├── mash_sketch_fasta.nf │ │ ├── mash_sketch_fastq.nf │ │ ├── maxbin2.nf │ │ ├── megahit.nf │ │ ├── metabat2.nf │ │ ├── metamlst.nf │ │ ├── metaprob.nf │ │ ├── metaspades.nf │ │ ├── midas_species.nf │ │ ├── mlst.nf │ │ ├── momps.nf │ │ ├── nextflow.config │ │ ├── params.config │ │ ├── patho_typing.nf │ │ ├── patlas_consensus.nf │ │ ├── pilon.nf │ │ ├── pipeline_graph.html │ │ ├── post.txt │ │ ├── process_skesa.nf │ │ ├── process_spades.nf │ │ ├── progressive_mauve.nf │ │ ├── prokka.nf │ │ ├── quast.nf │ │ ├── raxml.nf │ │ ├── reads_download.nf │ │ ├── remove_host.nf │ │ ├── report_compiler.nf │ │ ├── report_post.txt │ │ ├── resources.config │ │ ├── retrieve_mapped.nf │ │ ├── seq_typing.nf │ │ ├── seroba.nf │ │ ├── sistr.nf │ │ ├── skesa.nf │ │ ├── spades.nf │ │ ├── split_assembly.nf │ │ ├── status_compiler.nf │ │ ├── trace_compiler.nf │ │ ├── trimmomatic.nf │ │ ├── true_coverage.nf │ │ ├── unicycler.nf │ │ ├── user.config │ │ └── viral_assembly.nf │ └── utils.py ├── lib │ └── CheckParams.groovy ├── profiles.config ├── resources │ └── main.js.zip ├── templates │ ├── README.md │ ├── __init__.py │ ├── assembly_report.py │ ├── compile_reports.py │ ├── dengue_typing_assembly.py │ ├── dengue_typing_reads.py │ ├── downsample_fastq.py │ ├── fasta_spliter.py │ ├── fastqc.py │ ├── fastqc_report.py │ ├── flowcraft_utils │ │ ├── __init__.py │ │ └── flowcraft_base.py │ ├── integrity_coverage.py │ ├── mapping2json.py │ ├── mashdist2json.py │ ├── mashscreen2json.py │ ├── megahit.py │ ├── metaspades.py │ ├── pATLAS_consensus_json.py │ ├── pipeline_status.py │ ├── process_abricate.py │ ├── process_assembly.py │ ├── process_assembly_mapping.py │ ├── process_concoct.py │ ├── process_mapping.py │ ├── process_metabat.py │ ├── process_newick.py │ ├── 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