remove the database auto-download for mOTUs.

.github/workflows/ci.yml

@@ -42,8 +42,6 @@ jobs:
           - "--perform_runmerging"
           - "--perform_runmerging --shortread_qc_mergepairs"
           - "--shortread_complexityfilter false --perform_shortread_hostremoval"
-        # Test different profiles
-        profile: ["test", "test_motus"]
 
     steps:
       - name: Check out pipeline code
@@ -72,4 +70,54 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
+
+  motus:
+      name: Test mOTUs with workflow parameters
+      if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
+      runs-on: ubuntu-latest
+      env:
+        NXF_VER: ${{ matrix.nxf_ver }}
+        NXF_ANSI_LOG: false
+      strategy:
+        matrix:
+          # Nextflow versions
+          include:
+            # Test pipeline minimum Nextflow version
+            - NXF_VER: "21.10.3"
+              NXF_EDGE: ""
+            # Test latest edge release of Nextflow
+            - NXF_VER: ""
+              NXF_EDGE: "1"
+
+      steps:
+        - name: Check out pipeline code
+          uses: actions/checkout@v2
+
+        - name: Install Nextflow
+          env:
+            NXF_VER: ${{ matrix.NXF_VER }}
+            # Uncomment only if the edge release is more recent than the latest stable release
+            # See https://github.com/nextflow-io/nextflow/issues/2467
+            # NXF_EDGE: ${{ matrix.NXF_EDGE }}
+          run: |
+            wget -qO- get.nextflow.io | bash
+            sudo mv nextflow /usr/local/bin/
+
+        - name: Show current locale
+          run: locale
+
+        - name: Set UTF-8 enabled locale
+          run: |
+            sudo locale-gen en_US.UTF-8
+            sudo update-locale LANG=en_US.UTF-8
+
+        - name: Prepare the database
+          run: |
+            wget https://github.com/motu-tool/mOTUs/blob/master/motus/downloadDB.py
+            python downloadDB.py
+            echo 'tool,db_name,db_params,db_path\nmotus,db_mOTU,,db_mOTU' > 'database_motus.csv'
+
+        - name: Run pipeline with test data
+          run: |
+            nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv

conf/modules.config

@@ -353,13 +353,6 @@ process {
         ]
     }
 
-    withName: MOTUS_DOWNLOADDB {
-        publishDir = [
-            path: { "${params.outdir}/motus/db/${meta.db_name}" },
-            mode: params.publish_dir_mode
-        ]
-    }
-
     withName: MOTUS_PROFILE {
         publishDir = [
             path: { "${params.outdir}/motus/${meta.db_name}" },

conf/test_motus.config

@@ -23,7 +23,7 @@ params {
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
-    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
+    databases                             = 'database_motus.csv'
     perform_shortread_clipmerge           = false
     perform_longread_clip                 = false
     perform_shortread_complexityfilter    = false

docs/usage.md

@@ -138,8 +138,7 @@ Expected (uncompressed) database files for each tool are as follows:
   The database download step can be time consuming and the database will be consisting
   with same release version of the mOTUs tools. The database for same version tools
   can be thus reused for multiple runs. Users can download the database once and
-  assign the database with the table. User can also set the parameter
-  `download_motus_db` and let the pipeline download the database automatically.
+  assign the database with the table.
 
 ## Running the pipeline
 

modules.json

@@ -63,9 +63,6 @@
             "minimap2/index": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
-            "motus/downloaddb": {
-                "git_sha": "6393a085c5fcea11963774c041808df169907487"
-            },
             "motus/profile": {
                 "git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
             },

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

@@ -1,39 +0,0 @@
-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

@@ -1,39 +0,0 @@
-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"

nextflow.config

@@ -126,8 +126,6 @@ params {
 
     // 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

@@ -430,14 +430,6 @@
         },
         "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."
         }
     }
 }

subworkflows/local/db_check.nf

@@ -4,7 +4,6 @@
 
 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:
@@ -21,22 +20,6 @@ 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")