add motus profile.

conf/test.config

@@ -37,6 +37,7 @@ params {
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true
+    run_motus                             = true
 }
 
 process {

conf/test_nopreprocessing.config

@@ -37,6 +37,7 @@ params {
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true
+    run_motus                             = true
 }
 
 process {

conf/test_noprofiling.config

@@ -37,6 +37,7 @@ params {
     run_metaphlan3                        = false
     run_centrifuge                        = false
     run_diamond                           = false
+    run_motus                             = false
 }
 
 process {

modules.json

@@ -60,6 +60,12 @@
             "minimap2/index": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "motus/downloaddb": {
+                "git_sha": "6393a085c5fcea11963774c041808df169907487"
+            },
+            "motus/profile": {
+                "git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
+            },
             "multiqc": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
@@ -80,4 +86,4 @@
             }
         }
     }
-}
+}

modules/nf-core/modules/motus/downloaddb/main.nf

@@ -0,0 +1,39 @@
+process MOTUS_DOWNLOADDB {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
+        'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
+
+    input:
+    path motus_downloaddb_script
+
+    output:
+    path "db_mOTU/"                , emit: db
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args     = task.ext.args ?: ''
+    def software = "${motus_downloaddb_script.simpleName}_copy.py"
+    """
+    ## must copy script file to working directory,
+    ## otherwise the reference_db will be download to bin folder
+    ## other than current directory
+    cp $motus_downloaddb_script ${software}
+    python ${software} \\
+        $args \\
+        -t $task.cpus
+
+    ## mOTUs version number is not available from command line.
+    ## mOTUs save the version number in index database folder.
+    ## mOTUs will check the database version is same version as exec version.
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mOTUs: \$(grep motus db_mOTU/db_mOTU_versions | sed 's/motus\\t//g')
+    END_VERSIONS
+    """
+}

modules/nf-core/modules/motus/downloaddb/meta.yml

@@ -0,0 +1,39 @@
+name: "motus_downloaddb"
+description: Download the mOTUs database
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+  - database
+  - download
+tools:
+  - "motus":
+      description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
+      homepage: "None"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1038/s41467-019-08844-4"
+      licence: "['GPL v3']"
+
+input:
+  - motus_downloaddb:
+      type: directory
+      description: |
+        The mOTUs downloadDB script source file.
+        It is the source file installed or
+        remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
+      pattern: "downloadDB.py"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - db:
+      type: directory
+      description: The mOTUs database directory
+      pattern: "db_mOTU"
+
+authors:
+  - "@jianhong"

modules/nf-core/modules/motus/profile/main.nf

@@ -0,0 +1,54 @@
+process MOTUS_PROFILE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
+        'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path db
+
+    output:
+    tuple val(meta), path("*.out"), emit: out
+    tuple val(meta), path("*.bam"), optional: true, emit: bam
+    tuple val(meta), path("*.mgc"), optional: true, emit: mgc
+    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 inputs = reads[0].getExtension() == 'bam' ?
+                    "-i ${reads}" :
+                    reads[0].getExtension() == 'mgc' ? "-m $reads" :
+                        meta.single_end ?
+                            "-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
+    def refdb = db ? "-db ${db}" : ""
+    """
+    motus profile \\
+        $args \\
+        $inputs \\
+        $refdb \\
+        -t $task.cpus \\
+        -n $prefix \\
+        -o ${prefix}.out
+
+    ## mOTUs version number is not available from command line.
+    ## mOTUs save the version number in index database folder.
+    ## mOTUs will check the database version is same version as exec version.
+    if [ "$db" == "" ]; then
+        VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
+    else
+        VERSION=\$(grep motus $db/db_mOTU_versions | sed 's/motus\\t//g')
+    fi
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mOTUs: \$VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/modules/motus/profile/meta.yml

@@ -0,0 +1,61 @@
+name: "motus_profile"
+description: Taxonomic meta-omics profiling using universal marker genes
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+tools:
+  - "motus":
+      description: "Marker gene-based OTU (mOTU) profiling"
+      homepage: "https://motu-tool.org/"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1038/s41467-019-08844-4"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+        Or the intermediate bam file mapped by bwa to the mOTUs database or
+        the output bam file from motus profile.
+        Or the intermediate mgc read counts table.
+      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
+  - db:
+      type: directory
+      description: |
+        mOTUs database downloaded by `motus downloadDB`
+
+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"
+  - out:
+      type: file
+      description: Results with taxonomic classification of each read
+      pattern: "*.out"
+  - bam:
+      type: file
+      description: Optional intermediate sorted BAM file from BWA
+      pattern: "*.{bam}"
+  - mgc:
+      type: file
+      description: Optional intermediate mgc read count table file saved with `-M`.
+      pattern: "*.{mgc}"
+
+authors:
+  - "@jianhong"

nextflow.config

@@ -116,6 +116,11 @@ params {
     // diamond
     run_diamond                = false
     diamond_output_format      = 'txt'
+
+    // mOTUs
+    run_motus                  = false
+    download_motus_db          = true
+    motus_downloaddb_script    = 'https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'
 }
 
 // Load base.config by default for all pipelines

nextflow_schema.json

@@ -409,6 +409,17 @@
         "shortread_complexityfilter_fastp_threshold": {
             "type": "integer",
             "default": 30
+        },
+        "run_motus": {
+            "type": "boolean"
+        },
+        "download_motus_db": {
+            "type": "boolean"
+        },
+        "motus_downloaddb_script": {
+            "type": "string",
+            "default": "https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py",
+            "description": "mOTUs database download script path."
         }
     }
 }

null/pipeline_info/execution_trace_2022-05-21_11-05-12.txt

@@ -0,0 +1 @@
+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar

subworkflows/local/db_check.nf

@@ -2,8 +2,9 @@
 // Check input samplesheet and get read channels
 //
 
-include { DATABASE_CHECK } from '../../modules/local/database_check'
-include { UNTAR          } from '../../modules/nf-core/modules/untar/main'
+include { DATABASE_CHECK   } from '../../modules/local/database_check'
+include { UNTAR            } from '../../modules/nf-core/modules/untar/main'
+include { MOTUS_DOWNLOADDB } from '../../modules/nf-core/modules/motus/downloaddb/main'
 
 workflow DB_CHECK {
     take:
@@ -20,6 +21,22 @@ workflow DB_CHECK {
         .splitCsv ( header:true, sep:',' )
         .map { create_db_channels(it) }
 
+    // Download database for mOTUs
+    if( params.run_motus ){
+        check_motus_db =
+            parsed_samplesheet.filter{ it[0].tool == "motus" }
+                .ifEmpty{[]}
+        if( params.download_motus_db ){
+            MOTUS_DOWNLOADDB( params.motus_downloaddb_script )
+            check_motus_db = MOTUS_DOWNLOADDB.out.db
+                .map{[
+                    [tool: "motus", db_name: "db_mOTU", db_params: ''],
+                    it
+                ]}
+        }
+        parsed_samplesheet = parsed_samplesheet.mix(check_motus_db)
+    }
+
     ch_dbs_for_untar = parsed_samplesheet
         .branch {
             untar: it[1].toString().endsWith(".tar.gz")

subworkflows/local/profiling.nf

@@ -11,7 +11,7 @@ include { METAPHLAN3                  } from '../../modules/nf-core/modules/meta
 include { KAIJU_KAIJU                 } from '../../modules/nf-core/modules/kaiju/kaiju/main'
 include { KAIJU_KAIJU2TABLE           } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
 include { DIAMOND_BLASTX              } from '../../modules/nf-core/modules/diamond/blastx/main'
-
+include { MOTUS_PROFILE               } from '../../modules/nf-core/modules/motus/profile/main'
 
 workflow PROFILING {
     take:
@@ -44,6 +44,7 @@ workflow PROFILING {
                 centrifuge: it[2]['tool'] == 'centrifuge'
                 kaiju: it[2]['tool'] == 'kaiju'
                 diamond: it[2]['tool'] == 'diamond'
+                motus: it[2]['tool'] == 'motus'
                 unknown: true
             }
 
@@ -186,9 +187,23 @@ workflow PROFILING {
 
     }
 
+    if ( params.run_motus ) {
+
+        ch_input_for_motus = ch_input_for_profiling.motus
+                                .multiMap {
+                                    it ->
+                                        reads: [it[0] + it[2], it[1]]
+                                        db: it[3]
+                                }
+
+        MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
+        ch_versions        = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
+        ch_raw_profiles    = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
+
+    }
+
     emit:
     profiles = ch_raw_profiles    // channel: [ val(meta), [ reads ] ] - should be text files or biom
     versions = ch_versions          // channel: [ versions.yml ]
     mqc      = ch_multiqc_files
 }
-