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:false ]

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

profile

meta:map

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

*_profile.txt:file

Tab-separated output file of the predicted taxon relative abundances

*.{txt}

biom

meta:map

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

*.biom:file

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

*.{biom}

bt2out

meta:map

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

*.bowtie2out.txt:file

Bowtie2 output file

*.{bowtie2out.txt}

versions

versions.yml:file

File containing software versions

versions.yml

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
Github user MGordon09
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