nf-core_modules/modules/metaphlan3/meta.yml

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name: metaphlan3
description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
keywords:
- metagenomics
- classification
- fastq
- bam
- fasta
tools:
- metaphlan3:
description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
homepage: https://huttenhower.sph.harvard.edu/metaphlan/
documentation: https://github.com/biobakery/MetaPhlAn
doi: "10.7554/eLife.65088"
licence: ['MIT License']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)
pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- profile:
type: file
description: Tab-separated output file of the predicted taxon relative abundances
pattern: "*.{txt}"
- biom:
type: file
description: General-use format for representing biological sample by observation contingency tables
pattern: "*.{biom}"
- bowtie2out:
type: file
description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )
pattern: "*.{bowtie2out.txt}"
authors:
- "@MGordon09"