├── .devcontainer └── devcontainer.json ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix_linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── nf-test.yml │ ├── release-announcements.yml │ └── template-version-comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .vscode └── settings.json ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── email_template.html ├── email_template.txt ├── nf-core-genomeassembler_logo_light.png ├── report │ ├── _quarto-base.yml │ ├── _quarto-busco.yml │ ├── _quarto-jellyfish.yml │ ├── _quarto-meryl.yml │ ├── _quarto-nanoq.yml │ ├── _quarto-quast.yml │ ├── _quarto.yml │ ├── functions │ │ ├── plot_merqury.R │ │ ├── read_busco.R │ │ ├── read_genomescope.R │ │ ├── read_nanoq.R │ │ └── read_quast.R │ └── report.qmd ├── samplesheet.csv ├── samplesheets │ ├── test_input_channels.csv │ ├── test_input_channels.yml │ └── test_samplesheet.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── false_duplications.awk └── genomescope.R ├── conf ├── base.config ├── modules.config ├── modules │ ├── QC │ │ ├── alignments.config │ │ ├── busco.config │ │ ├── jellyfish-genomescope.config │ │ ├── merqury.config │ │ ├── meryl.config │ │ └── quast.config │ ├── assembly.config │ ├── hifi-prep.config │ ├── liftoff.config │ ├── ont-prep.config │ ├── polishing.config │ ├── report.config │ ├── scaffolding.config │ └── trimgalore.config ├── test.config ├── test_full.config ├── test_input_csv.config └── test_input_yml.config ├── configs ├── hifi_flye.config ├── hifi_hifiasm.config ├── hifi_ont_flye_on_hifiasm.config ├── hifi_ont_hifiasm_on_hifiasm.config ├── hifi_ont_hifiasm_ul.config ├── ont_flye.config └── ont_hifiasm.config ├── docs ├── README.md ├── images │ ├── genomeassembler.dark.png │ ├── genomeassembler.light.png │ ├── nf-core-genomeassembler_logo_dark.png │ └── nf-core-genomeassembler_logo_light.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── collect_reads │ │ ├── environment.yml │ │ └── main.nf │ ├── genomescope │ │ ├── environment.yml │ │ └── main.nf │ ├── gfa2fa │ │ ├── environment.yml │ │ └── main.nf │ ├── jellyfish │ │ ├── count │ │ │ ├── environment.yml │ │ │ └── main.nf │ │ ├── dump │ │ │ ├── environment.yml │ │ │ └── main.nf │ │ ├── histo │ │ │ ├── environment.yml │ │ │ └── main.nf │ │ └── stats │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── longstitch │ │ ├── environment.yml │ │ └── main.nf │ ├── medaka │ │ ├── main.nf │ │ └── medaka_consensus │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── nanoq │ │ ├── environment.yml │ │ └── main.nf │ ├── quast │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── report │ │ ├── environment.yml │ │ └── main.nf └── nf-core │ ├── busco │ └── busco │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── flye │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── hifiasm │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── liftoff │ ├── environment.yml │ ├── liftoff.diff │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── lima │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── links │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── merqury │ └── merqury │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── merqury-merqury.diff │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── meryl │ ├── count │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── unionsum │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── minimap2 │ └── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── minimap2-align.diff │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── pilon │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── porechop │ └── porechop │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── ragtag │ ├── patch │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── scaffold │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── samtools │ ├── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── flagstat │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── idxstats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── nextflow_cram.config │ └── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ └── trimgalore │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config ├── nextflow.config ├── nextflow_schema.json ├── nf-core-genomeassembler_logo_dark.svg ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── assemble │ │ └── main.nf │ ├── bam_sort_stat │ │ └── main.nf │ ├── hifi │ │ └── main.nf │ ├── jellyfish │ │ └── main.nf │ ├── liftoff │ │ └── main.nf │ ├── mapping │ │ ├── map_sr │ │ │ └── main.nf │ │ ├── map_to_assembly │ │ │ └── main.nf │ │ └── map_to_ref │ │ │ └── main.nf │ ├── ont │ │ └── main.nf │ ├── polishing │ │ ├── main.nf │ │ ├── medaka │ │ │ ├── polish_medaka │ │ │ │ └── main.nf │ │ │ └── run_medaka │ │ │ │ └── main.nf │ │ └── pilon │ │ │ ├── polish_pilon │ │ │ └── main.nf │ │ │ └── run_pilon │ │ │ └── main.nf │ ├── prepare_hifi │ │ └── main.nf │ ├── prepare_ont │ │ ├── chop │ │ │ └── main.nf │ │ ├── collect │ │ │ └── main.nf │ │ ├── main.nf │ │ └── run_nanoq │ │ │ └── main.nf │ ├── prepare_shortreads │ │ └── main.nf │ ├── qc │ │ ├── busco │ │ │ └── main.nf │ │ ├── main.nf │ │ ├── merqury │ │ │ └── main.nf │ │ └── quast │ │ │ └── main.nf │ ├── scaffolding │ │ ├── links │ │ │ └── main.nf │ │ ├── longstitch │ │ │ └── main.nf │ │ ├── main.nf │ │ └── ragtag │ │ │ └── main.nf │ └── utils_nfcore_genomeassembler_pipeline │ │ └── main.nf └── nf-core │ ├── bam_sort_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bam_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── 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