implemented chocophlan and uniref modules & tests

modules/local/humann/downloadchocophlandb/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::humann=3.8

modules/local/humann/downloadchocophlandb/main.nf

@@ -0,0 +1,47 @@
+process HUMANN_DOWNLOADCHOCOPHLANDB {
+    tag "${params.chocophlan_db_version}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/humann:3.8--pyh7cba7a3_0':
+        'quay.io/biocontainers/humann:3.8--pyh7cba7a3_0' }"
+
+    output:
+    path "${prefix}/chocophlan/"    , emit: chocophlan_db_dir
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "chocophlan_db_${params.chocophlan_db_version}"
+    """
+    mkdir -p ${prefix}
+
+    https_proxy=http://klone-dip1-A-ib:3128
+    export https_proxy
+    humann_databases \\
+        --download chocophlan ${params.chocophlan_db_version} \\
+        ${prefix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        humann: \$(echo \$(humann --version 2>&1 | sed 's/^.*humann //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "chocophlan_db_${params.chocophlan_db_version}"
+    """
+    mkdir -p ${prefix}/chocophlan/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        humann: \$(echo \$(humann --version 2>&1 | sed 's/^.*humann //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}

modules/local/humann/downloadchocophlandb/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: HUMANN_DOWNLOADCHOCOPHLANDB {
+        ext.args = "--update-config no"
+    }
+}

modules/local/humann/downloadchocophlandb/tests/main.nf.test

@@ -0,0 +1,46 @@
+nextflow_process {
+
+    name "Test Process: HUMANN_DOWNLOADCHOCOPHLANDB"
+    script "../main.nf"
+    process "HUMANN_DOWNLOADCHOCOPHLANDB"
+
+    tag "modules"
+    tag "modules_local"
+    tag "humann"
+    tag "humann/downloadchocophlandb"
+
+
+    test(" chocophlan_db_version = 'DEMO' ") {
+
+        when {
+            params {
+                chocophlan_db_version = 'DEMO'
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test(" chocophlan_db_version = 'DEMO' -stub ") {
+
+        options "-stub"
+
+        when {
+            params {
+                chocophlan_db_version = 'DEMO'
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/local/humann/downloadchocophlandb/tests/main.nf.test.snap

@@ -0,0 +1,58 @@
+{
+    " chocophlan_db_version = 'DEMO' ": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz:md5,c23ab47a3f0a34abd20f0b1826482c6d",
+                        "g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz:md5,61a2c5aa5ff04e400147974852e5bcc2"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3d4522d3366acea81c55007726662550"
+                ],
+                "chocophlan_db_dir": [
+                    [
+                        "g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz:md5,c23ab47a3f0a34abd20f0b1826482c6d",
+                        "g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz:md5,61a2c5aa5ff04e400147974852e5bcc2"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3d4522d3366acea81c55007726662550"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-16T13:49:34.969434147"
+    },
+    " chocophlan_db_version = 'DEMO' -stub ": {
+        "content": [
+            {
+                "0": [
+                    [
+
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3d4522d3366acea81c55007726662550"
+                ],
+                "chocophlan_db_dir": [
+                    [
+
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3d4522d3366acea81c55007726662550"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-16T13:49:44.337325581"
+    }
+}

modules/local/humann/downloadchocophlandb/tests/tags.yml

@@ -0,0 +1,2 @@
+humann/downloadchocophlandb:
+  - modules/local/humann/downloadchocophlandb/**

modules/local/humann/downloadunirefdb/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::humann=3.8

modules/local/humann/downloadunirefdb/main.nf

@@ -0,0 +1,47 @@
+process HUMANN_DOWNLOADUNIREFDB {
+    tag "${params.uniref_db_version}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/humann:3.8--pyh7cba7a3_0':
+        'quay.io/biocontainers/humann:3.8--pyh7cba7a3_0' }"
+
+    output:
+    path "${prefix}/uniref/"    , emit: uniref_db_dir
+    path "versions.yml"         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "uniref_db_${params.uniref_db_version}"
+    """
+    mkdir -p ${prefix}
+
+    https_proxy=http://klone-dip1-A-ib:3128
+    export https_proxy
+    humann_databases \\
+        --download uniref ${params.uniref_db_version} \\
+        ${prefix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        humann: \$(echo \$(humann --version 2>&1 | sed 's/^.*humann //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "uniref_db_${params.uniref_db_version}"
+    """
+    mkdir -p ${prefix}/uniref/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        humann: \$(echo \$(humann --version 2>&1 | sed 's/^.*humann //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}

modules/local/humann/downloadunirefdb/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: HUMANN_DOWNLOADUNIREFDB {
+        ext.args = "--update-config no"
+    }
+}

modules/local/humann/downloadunirefdb/tests/main.nf.test

@@ -0,0 +1,46 @@
+nextflow_process {
+
+    name "Test Process: HUMANN_DOWNLOADUNIREFDB"
+    script "../main.nf"
+    process "HUMANN_DOWNLOADUNIREFDB"
+
+    tag "modules"
+    tag "modules_local"
+    tag "humann"
+    tag "humann/downloadunirefdb"
+
+
+    test(" uniref_db_version = 'DEMO_diamond' ") {
+
+        when {
+            params {
+                uniref_db_version = 'DEMO_diamond'
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test(" uniref_db_version = 'DEMO_diamond' -stub ") {
+
+        options "-stub"
+
+        when {
+            params {
+                uniref_db_version = 'DEMO_diamond'
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/local/humann/downloadunirefdb/tests/main.nf.test.snap

@@ -0,0 +1,56 @@
+{
+    " uniref_db_version = 'DEMO_diamond' ": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "uniref90_demo_prots_v201901b.dmnd:md5,1d2f8df48a349d72436425aafa29a6b1"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9701558bc32dc67749aad70c9a67960f"
+                ],
+                "uniref_db_dir": [
+                    [
+                        "uniref90_demo_prots_v201901b.dmnd:md5,1d2f8df48a349d72436425aafa29a6b1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9701558bc32dc67749aad70c9a67960f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-16T14:04:05.712218097"
+    },
+    " uniref_db_version = 'DEMO_diamond' -stub ": {
+        "content": [
+            {
+                "0": [
+                    [
+
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9701558bc32dc67749aad70c9a67960f"
+                ],
+                "uniref_db_dir": [
+                    [
+
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9701558bc32dc67749aad70c9a67960f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-16T14:04:13.931593633"
+    }
+}

nextflow.config

@@ -28,6 +28,11 @@ params {
     metaphlan_options           = null
     metaphlan_sgb2gtbd_file     = "https://github.com/biobakery/MetaPhlAn/raw/master/metaphlan/utils/mpa_vOct22_CHOCOPhlAnSGB_202212_SGB2GTDB.tsv"
 
+    // HUMAnN options
+    chocophlan_db_version       ='DEMO'
+    uniref_db_version           ='DEMO_diamond'
+    utility_mapping_version     ='DEMO'
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -80,6 +85,9 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
+// Workflow specific configs
+includeConfig './workflows/biobakerymgx/nextflow.config'
+
 // Load hofflab/biobakerymgx custom profiles from different institutions.
 // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
 // try {

subworkflows/local/fastq_microbial_pathway_humann/nextflow.config

@@ -0,0 +1,2 @@
+includeConfig '../../../modules/local/humann/downloadchocophlandb/nextflow.config'
+includeConfig '../../../modules/local/humann/downloadunirefdb/nextflow.config'

workflows/biobakerymgx/nextflow.config

@@ -0,0 +1 @@
+includeConfig "../../subworkflows/local/fastq_microbial_pathway_humann/nextflow.config"