chore: add metaphlan3 module

modules.json

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

modules/nf-core/modules/metaphlan3/main.nf

@@ -0,0 +1,45 @@
+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
+    """
+}

modules/nf-core/modules/metaphlan3/meta.yml

@@ -0,0 +1,52 @@
+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"