modules/metaphlan3_metaphlan3

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

metagenomicsclassificationfastqbamfasta

https://github.com/nf-core/modules/[...]/modules/nf-core/metaphlan3/metaphlan3

Description

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

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`input{:bash}`
`: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{:bash}`
`: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{:bash}`

`meta{:bash}`
`:map`

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

`*_profile.txt{:bash}`
`:file`

Tab-separated output file of the predicted taxon relative abundances

*.{txt}

`biom{:bash}`

`meta{:bash}`
`:map`

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

`*.biom{:bash}`
`:file`

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

*.{biom}

`bt2out{:bash}`

`meta{:bash}`
`:map`

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

`*.bowtie2out.txt{:bash}`
`:file`

Bowtie2 output file

*.{bowtie2out.txt}

`versions{:bash}`

`versions.yml{:bash}`
`: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

modules/metaphlan3_metaphlan3

Description

Input

`meta{:bash}`
`:map`

`input{:bash}`
`:file`

`metaphlan_db{:bash}`
`:file`

Output

`profile{:bash}`

`meta{:bash}`
`:map`

`*_profile.txt{:bash}`
`:file`

`biom{:bash}`

`meta{:bash}`
`:map`

`*.biom{:bash}`
`:file`

`bt2out{:bash}`

`meta{:bash}`
`:map`

`*.bowtie2out.txt{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

metaphlan3
MIT License

maintainer

get in touch

modules/metaphlan3_metaphlan3

Description

Input

meta{:bash}:map

input{:bash}:file

metaphlan_db{:bash}:file

Output

profile{:bash}

meta{:bash}:map

*_profile.txt{:bash}:file

biom{:bash}

meta{:bash}:map

*.biom{:bash}:file

bt2out{:bash}

meta{:bash}:map

*.bowtie2out.txt{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

metaphlan3 MIT License

maintainer

get in touch

`meta{:bash}`
`:map`

`input{:bash}`
`:file`

`metaphlan_db{:bash}`
`:file`

`profile{:bash}`

`meta{:bash}`
`:map`

`*_profile.txt{:bash}`
`:file`

`biom{:bash}`

`meta{:bash}`
`:map`

`*.biom{:bash}`
`:file`

`bt2out{:bash}`

`meta{:bash}`
`:map`

`*.bowtie2out.txt{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

metaphlan3
MIT License