├── .devcontainer ├── devcontainer.json └── setup.sh ├── .gitattributes ├── .github ├── .dockstore.yml ├── CODEOWNERS ├── 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 │ ├── 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 ├── .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 ├── data │ ├── GCA_000840245.1_ViralProj14204_genomic.fna.gz │ └── GCA_002596845.1_ASM259684v1_genomic.fna.gz ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-mag_logo_light.png ├── schema_assembly_input.json ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── combine_tables.py ├── create_metabinner_bins.py ├── domain_classification.R ├── filter_ssu.py ├── get_mag_depths.py ├── get_mag_depths_summary.py ├── multiqc_to_custom_tsv.py ├── plot_mag_depths.py ├── prepare_bigmag_summary.py ├── split_fasta.py └── summary_gtdbtk.py ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── test.config ├── test_alternatives.config ├── test_assembly_input.config ├── test_full.config ├── test_hybrid.config ├── test_longreadonly.config ├── test_longreadonly_alternatives.config ├── test_minimal.config └── test_single_end.config ├── docs ├── README.md ├── images │ ├── mag_logo.png │ ├── mag_logo.svg │ ├── mag_logo_mascot_dark.png │ ├── mag_logo_mascot_dark.svg │ ├── mag_logo_mascot_light.png │ ├── mag_logo_mascot_light.svg │ ├── mag_logo_mascot_only.png │ ├── mag_logo_mascot_only.svg │ ├── mag_metromap_dark.png │ ├── mag_metromap_dark.svg │ ├── mag_metromap_light.png │ ├── mag_metromap_light.svg │ ├── mag_workflow_dark_v4_0_0.png │ ├── mag_workflow_dark_v4_0_0.svg │ ├── mag_workflow_v4_0_0.png │ ├── mag_workflow_v4_0_0.svg │ ├── nf-core-mag_logo_dark.png │ └── nf-core-mag_logo_light.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── adjust_maxbin2_ext │ │ ├── environment.yml │ │ └── main.nf │ ├── bigmag_summary │ │ ├── environment.yml │ │ └── main.nf │ ├── bin_summary │ │ ├── environment.yml │ │ └── main.nf │ ├── bowtie2_assembly_align │ │ ├── environment.yml │ │ └── main.nf │ ├── bowtie2_assembly_build │ │ ├── environment.yml │ │ └── main.nf │ ├── bowtie2_removal_align │ │ ├── environment.yml │ │ └── main.nf │ ├── bowtie2_removal_build │ │ ├── environment.yml │ │ └── main.nf │ ├── dastool_rename_post │ │ ├── environment.yml │ │ └── main.nf │ ├── dastool_rename_pre │ │ ├── environment.yml │ │ └── main.nf │ ├── gtdbtk_db_preparation │ │ ├── environment.yml │ │ └── main.nf │ ├── gtdbtk_summary │ │ ├── environment.yml │ │ └── main.nf │ ├── mag_depths │ │ ├── environment.yml │ │ └── main.nf │ ├── mag_depths_convert │ │ ├── environment.yml │ │ └── main.nf │ ├── mag_depths_plot │ │ ├── environment.yml │ │ └── main.nf │ ├── mag_depths_summary │ │ ├── environment.yml │ │ └── main.nf │ ├── metabinner_bins │ │ ├── environment.yml │ │ └── main.nf │ ├── metabinner_kmer │ │ ├── environment.yml │ │ └── main.nf │ ├── metabinner_metabinner │ │ ├── environment.yml │ │ └── main.nf │ ├── metabinner_tooshort │ │ ├── environment.yml │ │ └── main.nf │ ├── quast_bins │ │ ├── environment.yml │ │ └── main.nf │ ├── quast_bins_summary │ │ ├── environment.yml │ │ └── main.nf │ ├── quast_run │ │ ├── environment.yml │ │ └── main.nf │ ├── samtools_unmapped │ │ ├── environment.yml │ │ └── main.nf │ ├── split_fasta │ │ ├── environment.yml │ │ └── main.nf │ └── tiara_classify │ │ ├── environment.yml │ │ └── main.nf └── nf-core │ ├── adapterremoval │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── bbmap │ └── bbnorm │ │ ├── bbmap-bbnorm.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── bcftools │ ├── consensus │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── view │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── vcf_gz_index.config │ │ ├── vcf_gz_index_csi.config │ │ └── vcf_gz_index_tbi.config │ ├── busco │ └── busco │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── cat │ └── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── catpack │ ├── addnames │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── bins │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── contigs │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── download │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── prepare │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── summarise │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── checkm │ ├── lineagewf │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── qa │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── checkm2 │ ├── databasedownload │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── predict │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── chopper │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── comebin │ └── runcomebin │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── concoct │ ├── concoct │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── concoctcoveragetable │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── cutupfasta │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── extractfastabins │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── mergecutupclustering │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── dastool │ ├── dastool │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── fastatocontig2bin │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── fastp │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.interleaved.config │ │ └── nextflow.save_failed.config │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── filtlong │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── flye │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── freebayes │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── genomad │ ├── download │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── endtoend │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── gtdbtk │ └── classifywf │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── gunc │ ├── downloaddb │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── mergecheckm │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── run │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── maxbin2 │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── megahit │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── metabat2 │ ├── jgisummarizebamcontigdepths │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── metabat2 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── metaeuk │ └── easypredict │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── metamdbg │ └── asm │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── minimap2 │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── mmseqs │ └── databases │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── nanolyse │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── nanoplot │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yaml │ ├── nanoq │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── porechop │ ├── abi │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── porechop │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── prodigal │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── prokka │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── pydamage │ ├── analyze │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── filter │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── qsv │ └── cat │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── samtools │ ├── faidx │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── nextflow2.config │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── semibin │ └── singleeasybin │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── semibin-singleeasybin.diff │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── seqkit │ └── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── seqtk │ └── mergepe │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── spades │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── tiara │ └── tiara │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── trimmomatic │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow_PE.config │ │ └── nextflow_SE.config │ └── untar │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── tests │ ├── main.nf.test │ └── main.nf.test.snap │ └── untar.diff ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── ancient_dna │ │ ├── main.nf │ │ └── meta.yml │ ├── assembly │ │ ├── main.nf │ │ └── meta.yml │ ├── assembly_hybrid │ │ ├── main.nf │ │ └── meta.yml │ ├── assembly_longread │ │ ├── main.nf │ │ └── meta.yml │ ├── assembly_shortread │ │ ├── main.nf │ │ └── meta.yml │ ├── bin_qc │ │ ├── main.nf │ │ └── meta.yml │ ├── binning │ │ ├── main.nf │ │ └── meta.yml │ ├── binning_metabinner │ │ ├── main.nf │ │ └── meta.yml │ ├── binning_preparation │ │ ├── main.nf │ │ └── meta.yml │ ├── binning_preparation_longread │ │ ├── main.nf │ │ └── meta.yml │ ├── binning_preparation_shortread │ │ ├── main.nf │ │ └── meta.yml │ ├── binning_refinement │ │ ├── main.nf │ │ └── meta.yml │ ├── catpack │ │ ├── main.nf │ │ └── meta.yml │ ├── depths │ │ ├── main.nf │ │ └── meta.yml │ ├── domain_classification │ │ ├── main.nf │ │ └── meta.yml │ ├── gtdbtk │ │ ├── main.nf │ │ └── meta.yml │ ├── hostremoval_longread │ │ ├── main.nf │ │ └── meta.yml │ ├── preprocessing_longread │ │ ├── main.nf │ │ └── meta.yml │ ├── preprocessing_shortread │ │ ├── main.nf │ │ └── meta.yml │ ├── tiara │ │ ├── main.nf │ │ └── meta.yml │ ├── utils_nfcore_mag_pipeline │ │ ├── main.nf │ │ └── meta.yml │ └── virus_identification │ │ ├── main.nf │ │ └── meta.yml └── nf-core │ ├── fasta_binning_concoct │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ └── nextflow.config │ ├── utils_nfcore_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── main.workflow.nf.test.snap │ │ └── nextflow.config │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── tests ├── .nftignore ├── default.nf.test ├── default.nf.test.snap ├── nextflow.config ├── test_alternatives.nf.test ├── test_alternatives.nf.test.snap ├── test_assembly_input.nf.test ├── test_assembly_input.nf.test.snap ├── test_hybrid.nf.test ├── test_hybrid.nf.test.snap ├── test_longreadonly.nf.test ├── test_longreadonly.nf.test.snap ├── test_longreadonly_alternatives.nf.test ├── test_longreadonly_alternatives.nf.test.snap ├── test_minimal.nf.test ├── test_minimal.nf.test.snap ├── test_single_end.nf.test 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