humann3

modules/humann/main.nf

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+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process HUMANN {
+    tag "$meta.id"
+    label 'process_low'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda (params.enable_conda ? "bioconda::humann=3.0.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/humann:3.0.0--pyh5e36f6f_1':
+        'quay.io/biocontainers/humann:3.0.0--pyh5e36f6f_1' }"
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    tuple val(meta), path(sample), path(nt),path(protein),path(metadb)   
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("outdir"), emit: outdir
+    // TODO nf-core: List additional required output channels/values here
+    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}"
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    """
+    humann \\
+        -o outdir \\
+        --threads $task.cpus \\
+        -i $sample \\
+        --nucleotide-database $nt \\
+        --protein-database $protein \\
+        --metaphlan-options "-x $prefix --bowtie2db $metadb "
+
+
+    cat <<-END_VERSIONS > versions.yml
+        humann: \$(echo \$(humann --version 2>&1)  )
+    END_VERSIONS
+
+    """
+}

modules/humann/meta.yml

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+name: "humann"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "humann":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "HUMAnN: The HMP Unified Metabolic Analysis Network, version 3"
+      homepage: "http://huttenhower.sph.harvard.edu/humann"
+      documentation: "http://huttenhower.sph.harvard.edu/humann"
+      tool_dev_url: "https://github.com/biobakery/humann"
+      doi: ""
+      licence: "['MIT']"
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  # 
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  #Only when we have meta
+  - 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"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@kohjy-ag"

tests/modules/humann/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HUMANN } from '../../../modules/humann/main.nf'
+
+workflow test_humann {
+
+    input = [
+    	      [ id:'mpa_v30_CHOCOPhlAn_201901' ], // meta map
+              file('https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/qiaseq/SRR7545951-small_1.fastq.gz', checkIfExists: true),
+              file('chocophlan', checkIfExists: true),
+              file('uniref', checkIfExists: true),
+              file('metaphlandb', checkIfExists: true)
+    ]
+
+    HUMANN ( input )
+}

tests/modules/humann/nextflow.config

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+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/humann/test.yml

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+- name: humann test_humann
+  command: nextflow run tests/modules/humann -entry test_humann -c tests/config/nextflow.config
+  tags:
+    - humann
+  files:
+    - path: output/humann/versions.yml
+      md5sum: f6ffecc08eaf8ab67253798065a54158