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chore: add metaphlan3 module

This commit is contained in:
Moritz E. Beber 2022-03-18 15:38:19 +01:00
parent 1dfbcacf68
commit 4d2960c06f
3 changed files with 100 additions and 0 deletions

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@ -24,6 +24,9 @@
"malt/run": {
"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
},
"metaphlan3": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"multiqc": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},

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process METAPHLAN3 {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
input:
tuple val(meta), path(input)
path metaphlan_db
output:
tuple val(meta), path("*_profile.txt") , emit: profile
tuple val(meta), path("*.biom") , emit: biom
tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
"""
metaphlan \\
--nproc $task.cpus \\
$input_type \\
$input_data \\
$args \\
$bowtie2_out \\
--bowtie2db ${metaphlan_db} \\
--biom ${prefix}.biom \\
--output_file ${prefix}_profile.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
END_VERSIONS
"""
}

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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 ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- 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"