Workflows

Note

Mirrored from the MetaGEAR Pipeline repository: docs/workflows/index.md (db08c99). Check there directly for up-to-date information.

The schirmer-lab/metagear pipeline groups its work into five entry-point workflows, selected at run time with the --workflow parameter:

Workflow	Purpose	Input	Output	Cost
download_databases	One-time install of KneadData, MetaPhlAn, and HUMAnN references	—	Reference databases at the paths you supply	Disk + network
qc_dna	Adapter/quality trimming and host decontamination of DNA reads	Raw DNA FASTQ	Clean paired reads + QC report	Medium
qc_rna	Same flow as qc_dna; intended for metatranscriptomic input	Raw RNA FASTQ	Clean paired reads + QC report	Medium
microbial_profiles	Reference-based taxonomic and functional profiling	Clean reads	MetaPhlAn4 species table + HUMAnN3 gene-family and pathway tables	Medium–High
gene_analysis	De novo assembly, gene catalog, MSP analysis	Clean reads	Gene/protein catalogs, abundance matrices, MSPs	High

Recommended order

Run download_databases once per machine, then quality-control the raw reads, then choose whichever downstream workflows match your scientific question. The two analysis workflows (microbial_profiles, gene_analysis) are complementary and can run on the same QC’d reads.

# 1. One-time database setup
nextflow run schirmer-lab/metagear -profile docker \
  --workflow download_databases --outdir databases/

# 2. QC the raw reads
nextflow run schirmer-lab/metagear -profile docker \
  --workflow qc_dna --input raw.csv --outdir qc/

# 3. Pick one or both analyses
nextflow run schirmer-lab/metagear -profile docker \
  --workflow microbial_profiles --input clean.csv --outdir profiles/

nextflow run schirmer-lab/metagear -profile docker \
  --workflow gene_analysis --input clean.csv --outdir genes/

Picking a workflow

• Which organisms are present, and what functions can they perform? → microbial_profiles (reference-based, no assembly, fast).
• What genes are in this sample, including novel ones? → gene_analysis (assembly-based, captures genes absent from reference databases, builds metagenomic species pangenomes).

Input samplesheet

All workflows except download_databases take a CSV samplesheet via --input. Columns: sample, fastq_1, fastq_2 (R2 optional for single-end). See usage.md for the full samplesheet contract.

Wrapper CLI

The metagear-tools CLI wraps these workflows so that day-to-day invocations look like metagear qc_dna --input samples.csv. The pipeline runs identically with or without the wrapper; the Nextflow invocations shown here are the canonical form.