# muneebdev7/metabolt architecture

> Architecture diagram of the GitHub repository muneebdev7/metabolt, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-26). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/muneebdev7/metabolt
- Repository: https://github.com/muneebdev7/metabolt

## Overview

MDL/MetaBolt is a Nextflow pipeline for de novo metagenome assembly and binning. The documented workflow accepts a samplesheet of FASTQ reads, performs read QC and preprocessing, assembly, alignment and BAM processing, then calculates contig depth and bins contigs; MultiQC reports raw-read QC. The README documents the stage order, but no source excerpts were available to verify detailed channel wiring or internal calls, so the graph reflects only those documented relationships.

Main entry points: [`workflows/metabolt.nf`](https://github.com/muneebdev7/metabolt/blob/master/workflows/metabolt.nf) (MetaBolt workflow), [`main.nf`](https://github.com/muneebdev7/metabolt/blob/master/main.nf) (Nextflow entry), [`assets/samplesheet.csv`](https://github.com/muneebdev7/metabolt/blob/master/assets/samplesheet.csv) (FASTQ samplesheet), [`modules/nf-core/fastqc/main.nf`](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/fastqc/main.nf) (Read QC)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_entry["Pipeline entry"]
  node_entrypoint["Nextflow entry<br/>[main.nf]"]
  node_workflow["MetaBolt workflow<br/>[metabolt.nf]"]
end

subgraph group_reads["Read preparation"]
  node_samplesheet["FASTQ samplesheet<br/>[samplesheet.csv]"]
  node_fastqc["Read QC<br/>[main.nf]"]
  node_fastp["Read preprocessing<br/>[main.nf]"]
end

subgraph group_assembly["Assembly and alignment"]
  node_megahit["Metagenome assembly<br/>[main.nf]"]
  node_bwa_index["BWA indexing<br/>[main.nf]"]
  node_bwa_mem["Read mapping<br/>[main.nf]"]
  node_samtools["BAM processing"]
end

subgraph group_binning["Depth and binning"]
  node_depth["Contig depth<br/>[main.nf]"]
  node_metabat["Metagenome binning<br/>[main.nf]"]
end

subgraph group_reporting["Reporting"]
  node_multiqc["Read QC report<br/>[main.nf]"]
end

node_user(("Pipeline user"))

node_user -->|"runs"| node_entrypoint
node_entrypoint -->|"starts"| node_workflow
node_samplesheet -->|"provides reads"| node_workflow
node_workflow -->|"runs first"| node_fastqc
node_workflow -->|"preprocesses reads"| node_fastp
node_workflow -->|"assembles reads"| node_megahit
node_workflow -->|"indexes reference"| node_bwa_index
node_workflow -->|"maps reads"| node_bwa_mem
node_workflow -->|"processes alignments"| node_samtools
node_workflow -->|"calculates depth"| node_depth
node_workflow -->|"bins contigs"| node_metabat
node_workflow -->|"reports read QC"| node_multiqc

click node_entrypoint "https://github.com/muneebdev7/metabolt/blob/master/main.nf"
click node_workflow "https://github.com/muneebdev7/metabolt/blob/master/workflows/metabolt.nf"
click node_samplesheet "https://github.com/muneebdev7/metabolt/blob/master/assets/samplesheet.csv"
click node_fastqc "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/fastqc/main.nf"
click node_fastp "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/fastp/main.nf"
click node_megahit "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/megahit/main.nf"
click node_bwa_index "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/bwa/index/main.nf"
click node_bwa_mem "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/bwa/mem/main.nf"
click node_samtools "https://github.com/muneebdev7/metabolt/tree/master/modules/nf-core/samtools"
click node_depth "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf"
click node_metabat "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/metabat2/metabat2/main.nf"
click node_multiqc "https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/multiqc/main.nf"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_entrypoint,node_workflow,node_user toneBlue
class node_samplesheet,node_fastqc,node_fastp toneAmber
class node_megahit,node_bwa_index,node_bwa_mem,node_samtools toneMint
class node_depth,node_metabat toneRose
class node_multiqc toneIndigo
```

## Components

### Pipeline entry

- [Nextflow entry](https://github.com/muneebdev7/metabolt/blob/master/main.nf): `main.nf`
- [MetaBolt workflow](https://github.com/muneebdev7/metabolt/blob/master/workflows/metabolt.nf): `workflows/metabolt.nf`

### Read preparation

- [FASTQ samplesheet](https://github.com/muneebdev7/metabolt/blob/master/assets/samplesheet.csv): `assets/samplesheet.csv`
- [Read QC](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/fastqc/main.nf): `modules/nf-core/fastqc/main.nf`
- [Read preprocessing](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/fastp/main.nf): `modules/nf-core/fastp/main.nf`

### Assembly and alignment

- [Metagenome assembly](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/megahit/main.nf): `modules/nf-core/megahit/main.nf`
- [BWA indexing](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/bwa/index/main.nf): `modules/nf-core/bwa/index/main.nf`
- [Read mapping](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/bwa/mem/main.nf): `modules/nf-core/bwa/mem/main.nf`
- [BAM processing](https://github.com/muneebdev7/metabolt/tree/master/modules/nf-core/samtools): `modules/nf-core/samtools`

### Depth and binning

- [Contig depth](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf): `modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf`
- [Metagenome binning](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/metabat2/metabat2/main.nf): `modules/nf-core/metabat2/metabat2/main.nf`

### Reporting

- [Read QC report](https://github.com/muneebdev7/metabolt/blob/master/modules/nf-core/multiqc/main.nf): `modules/nf-core/multiqc/main.nf`

### Other components

- **Pipeline user**

## Connections

- Pipeline user → Nextflow entry: runs
- Nextflow entry → MetaBolt workflow: starts
- FASTQ samplesheet → MetaBolt workflow: provides reads
- MetaBolt workflow → Read QC: runs first
- MetaBolt workflow → Read preprocessing: preprocesses reads
- MetaBolt workflow → Metagenome assembly: assembles reads
- MetaBolt workflow → BWA indexing: indexes reference
- MetaBolt workflow → Read mapping: maps reads
- MetaBolt workflow → BAM processing: processes alignments
- MetaBolt workflow → Contig depth: calculates depth
- MetaBolt workflow → Metagenome binning: bins contigs
- MetaBolt workflow → Read QC report: reports read QC