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chore: add metaphlan3 module
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3 changed files with 100 additions and 0 deletions
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@ -24,6 +24,9 @@
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"malt/run": {
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"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
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},
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"metaphlan3": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"multiqc": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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45
modules/nf-core/modules/metaphlan3/main.nf
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45
modules/nf-core/modules/metaphlan3/main.nf
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process METAPHLAN3 {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
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'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
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input:
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tuple val(meta), path(input)
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path metaphlan_db
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output:
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tuple val(meta), path("*_profile.txt") , emit: profile
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tuple val(meta), path("*.biom") , emit: biom
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tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
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def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
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def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
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"""
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metaphlan \\
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--nproc $task.cpus \\
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$input_type \\
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$input_data \\
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$args \\
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$bowtie2_out \\
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--bowtie2db ${metaphlan_db} \\
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--biom ${prefix}.biom \\
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--output_file ${prefix}_profile.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
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END_VERSIONS
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"""
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}
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52
modules/nf-core/modules/metaphlan3/meta.yml
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modules/nf-core/modules/metaphlan3/meta.yml
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name: metaphlan3
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description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
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keywords:
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- metagenomics
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- classification
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- fastq
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- bam
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- fasta
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tools:
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- metaphlan3:
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description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
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homepage: https://huttenhower.sph.harvard.edu/metaphlan/
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documentation: https://github.com/biobakery/MetaPhlAn
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doi: "10.7554/eLife.65088"
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licence: ["MIT License"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input:
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type: file
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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)
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pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- profile:
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type: file
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description: Tab-separated output file of the predicted taxon relative abundances
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pattern: "*.{txt}"
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- biom:
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type: file
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description: General-use format for representing biological sample by observation contingency tables
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pattern: "*.{biom}"
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- bowtie2out:
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type: file
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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 )
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pattern: "*.{bowtie2out.txt}"
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authors:
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- "@MGordon09"
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