LICENSE
README.md
setup.cfg
setup.py
flowcraft/__init__.py
flowcraft/flowcraft.py
flowcraft/nextflow.config
flowcraft/profiles.config
flowcraft.egg-info/PKG-INFO
flowcraft.egg-info/SOURCES.txt
flowcraft.egg-info/dependency_links.txt
flowcraft.egg-info/entry_points.txt
flowcraft.egg-info/requires.txt
flowcraft.egg-info/top_level.txt
flowcraft/bin/final_POST.sh
flowcraft/bin/merge_json.py
flowcraft/bin/metadata_POST.sh
flowcraft/bin/parse_fasta.py
flowcraft/bin/parse_true_coverage.py
flowcraft/bin/prepare_reports.py
flowcraft/bin/renamePE_samtoolsFASTQ.py
flowcraft/bin/report_POST.sh
flowcraft/bin/set_dotfiles.sh
flowcraft/bin/startup_POST.sh
flowcraft/generator/__init__.py
flowcraft/generator/engine.py
flowcraft/generator/error_handling.py
flowcraft/generator/footer_skeleton.py
flowcraft/generator/header_skeleton.py
flowcraft/generator/inspect.py
flowcraft/generator/pipeline_parser.py
flowcraft/generator/process.py
flowcraft/generator/process_collector.py
flowcraft/generator/process_details.py
flowcraft/generator/recipe.py
flowcraft/generator/report.py
flowcraft/generator/components/__init__.py
flowcraft/generator/components/alignment.py
flowcraft/generator/components/annotation.py
flowcraft/generator/components/assembly.py
flowcraft/generator/components/assembly_processing.py
flowcraft/generator/components/distance_estimation.py
flowcraft/generator/components/downloads.py
flowcraft/generator/components/mapping.py
flowcraft/generator/components/metagenomics.py
flowcraft/generator/components/mlst.py
flowcraft/generator/components/patlas_mapping.py
flowcraft/generator/components/phylogeny.py
flowcraft/generator/components/reads_quality_control.py
flowcraft/generator/components/typing.py
flowcraft/generator/recipes/__init__.py
flowcraft/generator/recipes/denim.py
flowcraft/generator/recipes/innuca.py
flowcraft/generator/recipes/plasmids.py
flowcraft/generator/templates/Helper.groovy
flowcraft/generator/templates/abricate.nf
flowcraft/generator/templates/abyss.nf
flowcraft/generator/templates/assembly_mapping.nf
flowcraft/generator/templates/bandage.nf
flowcraft/generator/templates/bcalm.nf
flowcraft/generator/templates/bowtie.nf
flowcraft/generator/templates/card_rgi.nf
flowcraft/generator/templates/check_coverage.nf
flowcraft/generator/templates/chewbbaca.nf
flowcraft/generator/templates/compiler_channels.txt
flowcraft/generator/templates/containers.config
flowcraft/generator/templates/dengue_typing.nf
flowcraft/generator/templates/diamond.nf
flowcraft/generator/templates/downsample_fastq.nf
flowcraft/generator/templates/fast_ani.nf
flowcraft/generator/templates/fasterq_dump.nf
flowcraft/generator/templates/fastqc.nf
flowcraft/generator/templates/fastqc_trimmomatic.nf
flowcraft/generator/templates/filter_poly.nf
flowcraft/generator/templates/init.nf
flowcraft/generator/templates/integrity_coverage.nf
flowcraft/generator/templates/kraken.nf
flowcraft/generator/templates/mafft.nf
flowcraft/generator/templates/mapping_patlas.nf
flowcraft/generator/templates/mash_dist.nf
flowcraft/generator/templates/mash_screen.nf
flowcraft/generator/templates/mash_sketch_fasta.nf
flowcraft/generator/templates/mash_sketch_fastq.nf
flowcraft/generator/templates/maxbin2.nf
flowcraft/generator/templates/megahit.nf
flowcraft/generator/templates/metamlst.nf
flowcraft/generator/templates/metaprob.nf
flowcraft/generator/templates/metaspades.nf
flowcraft/generator/templates/midas_species.nf
flowcraft/generator/templates/mlst.nf
flowcraft/generator/templates/momps.nf
flowcraft/generator/templates/params.config
flowcraft/generator/templates/patho_typing.nf
flowcraft/generator/templates/patlas_consensus.nf
flowcraft/generator/templates/pilon.nf
flowcraft/generator/templates/pipeline_graph.html
flowcraft/generator/templates/post.txt
flowcraft/generator/templates/process_skesa.nf
flowcraft/generator/templates/process_spades.nf
flowcraft/generator/templates/progressive_mauve.nf
flowcraft/generator/templates/prokka.nf
flowcraft/generator/templates/quast.nf
flowcraft/generator/templates/raxml.nf
flowcraft/generator/templates/reads_download.nf
flowcraft/generator/templates/remove_host.nf
flowcraft/generator/templates/report_compiler.nf
flowcraft/generator/templates/report_post.txt
flowcraft/generator/templates/resources.config
flowcraft/generator/templates/retrieve_mapped.nf
flowcraft/generator/templates/seq_typing.nf
flowcraft/generator/templates/sistr.nf
flowcraft/generator/templates/skesa.nf
flowcraft/generator/templates/spades.nf
flowcraft/generator/templates/split_assembly.nf
flowcraft/generator/templates/status_compiler.nf
flowcraft/generator/templates/trace_compiler.nf
flowcraft/generator/templates/trimmomatic.nf
flowcraft/generator/templates/true_coverage.nf
flowcraft/generator/templates/unicycler.nf
flowcraft/generator/templates/user.config
flowcraft/generator/templates/viral_assembly.nf
flowcraft/lib/CheckParams.groovy
flowcraft/resources/main.js.zip
flowcraft/templates/__init__.py
flowcraft/templates/assembly_report.py
flowcraft/templates/compile_reports.py
flowcraft/templates/downsample_fastq.py
flowcraft/templates/fasta_spliter.py
flowcraft/templates/fastqc.py
flowcraft/templates/fastqc_report.py
flowcraft/templates/integrity_coverage.py
flowcraft/templates/mapping2json.py
flowcraft/templates/mashdist2json.py
flowcraft/templates/mashscreen2json.py
flowcraft/templates/megahit.py
flowcraft/templates/metaspades.py
flowcraft/templates/pATLAS_consensus_json.py
flowcraft/templates/pipeline_status.py
flowcraft/templates/process_abricate.py
flowcraft/templates/process_assembly.py
flowcraft/templates/process_assembly_mapping.py
flowcraft/templates/process_mapping.py
flowcraft/templates/process_newick.py
flowcraft/templates/process_viral_assembly.py
flowcraft/templates/skesa.py
flowcraft/templates/spades.py
flowcraft/templates/split_fasta.py
flowcraft/templates/trimmomatic.py
flowcraft/templates/trimmomatic_report.py
flowcraft/templates/flowcraft_utils/__init__.py
flowcraft/templates/flowcraft_utils/flowcraft_base.py