├── .github └── workflows │ ├── docker-dev.yml │ ├── docker-publish.yml │ ├── docker-release.yml │ └── issues_stale.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── assets ├── bbmap │ ├── nextera.fa.gz │ ├── nextera_LMP_adapter.fa.gz │ ├── nextera_LMP_linker.fa.gz │ ├── phix174_ill.ref.fa.gz │ ├── phix_adapters.fa.gz │ ├── truseq.fa.gz │ └── truseq_rna.fa.gz ├── ikmblogo.png └── multiqc_config.yaml ├── bin ├── collectmapping.R ├── contigfilterbylen.py ├── coverage_table.R ├── get_count_table.py ├── kraken2yaml.pl ├── merge_MAG_abundance.R ├── merge_abs_reads.py ├── merge_rel_reads.py └── salmon_merging.R ├── conf ├── base.config ├── biomedinf.config ├── caucluster.config ├── custom.config ├── googlebatch.config ├── local.config ├── medcluster.config └── quickstart.config ├── docs ├── hostgenome.md ├── installation.md ├── output.md ├── pipeline.md └── usage.md ├── environment.yml ├── images ├── TOFU-MAaPO_dag.svg ├── metawo_dag.svg └── tofu_overview.svg ├── lib ├── WorkflowCheck.groovy └── WorkflowHeaderHelp.groovy ├── main.nf ├── modules ├── QC │ ├── bbduk.nf │ ├── bowtie2.nf │ ├── collect.nf │ ├── download_host.nf │ ├── fastp.nf │ ├── fastqc.nf │ └── multiqc.nf ├── assembly │ ├── assembly_util.nf │ ├── bincoverage_persample.nf │ ├── bowtie2_contigs_mapping.nf │ ├── checkm.nf │ ├── concoct.nf │ ├── contig_filter.nf │ ├── gtdbtk.nf │ ├── magscot.nf │ ├── maxbin2.nf │ ├── megahit.nf │ ├── metabat.nf │ ├── minimap2_mapping.nf │ ├── semibin.nf │ └── vamb.nf ├── download.nf ├── entrez.nf ├── humann.nf ├── kraken.nf ├── metaphlan.nf ├── metaspades.nf ├── salmon.nf ├── software_versions.nf └── sylph.nf ├── nextflow.config ├── subworkflows ├── QC.nf ├── assembly.nf ├── humann.nf ├── input_check.nf ├── kraken.nf ├── metaphlan.nf ├── salmon.nf └── sylph.nf ├── utils └── prepare_input_csv.sh └── workflows ├── tofumaapo.nf └── tofumaapo_sylph.nf /.github/workflows/docker-dev.yml: 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