How muneebdev7/metabolt works
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: metabolt.nf MetaBolt workflow · main.nf Nextflow entry · samplesheet.csv FASTQ samplesheet · fastqc/main.nf Read QC
Components 13
Pipeline entry
- Nextflow entry
main.nf - MetaBolt workflow
workflows/metabolt.nf
Read preparation
- FASTQ samplesheet
assets/samplesheet.csv - Read QC
modules/nf-core/fastqc/main.nf - Read preprocessing
modules/nf-core/fastp/main.nf
Assembly and alignment
- Metagenome assembly
modules/nf-core/megahit/main.nf - BWA indexing
modules/nf-core/bwa/index/main.nf - Read mapping
modules/nf-core/bwa/mem/main.nf - BAM processing
modules/nf-core/samtools
Depth and binning
- Contig depth
modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf - Metagenome binning
modules/nf-core/metabat2/metabat2/main.nf
Reporting
- Read QC report
modules/nf-core/multiqc/main.nf
Other components
- Pipeline user
Connections 12
- 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