Description

MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input (file)

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)

*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}

metaphlan_db (file)

Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.
Note that you will also need to specify --index and the database version name (e.g. ‘mpa_v31_CHOCOPhlAn_201901’) in your module.conf ext.args for METAPHLAN3_METAPHLAN3!

*/

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

profile (file)

Tab-separated output file of the predicted taxon relative abundances

*.{txt}

biom (file)

General-use format for representing biological sample by observation contingency tables

*.{biom}

bowtie2out (file)

Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with bowtie2out files generated with MetaPhlAn versions below 3 )

*.{bowtie2out.txt}
author
Github user MGordon09
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Tools

metaphlan3
MIT License

Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance

huttenhower.sph.harvard.edu/metaphlan github.com/biobakery/MetaPhlAn 10.7554/eLife.65088