Add nf-test to metaphlan

modules/nf-core/metaphlan/mergemetaphlantables/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::metaphlan=4.0.6
+  - bioconda::metaphlan=4.1.1

modules/nf-core/metaphlan/mergemetaphlantables/main.nf

@@ -3,8 +3,8 @@ process METAPHLAN_MERGEMETAPHLANTABLES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/metaphlan:4.0.6--pyhca03a8a_0' :
-        'biocontainers/metaphlan:4.0.6--pyhca03a8a_0' }"
+        'https://depot.galaxyproject.org/singularity/metaphlan:4.1.1--pyhdfd78af_0' :
+        'biocontainers/metaphlan:4.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(profiles)
@@ -30,4 +30,16 @@ process METAPHLAN_MERGEMETAPHLANTABLES {
         metaphlan: \$(metaphlan --version 2>&1 | awk '{print \$3}')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        metaphlan: \$(metaphlan --version 2>&1 | awk '{print \$3}')
+    END_VERSIONS
+    """
 }

modules/nf-core/metaphlan/mergemetaphlantables/tests/main.nf.test

@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process METAPHLAN_MERGEMETAPHLANTABLES"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "METAPHLAN_MERGEMETAPHLANTABLES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untar"
+    tag "metaphlan"
+    tag "metaphlan/metaphlan"
+    tag "metaphlan/mergemetaphlantables"
+
+    setup {
+        run("UNTAR") {
+            script "../../../untar/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [],
+                    file( params.modules_testdata_base_path + 'delete_me/metaphlan4_database.tar.gz', checkIfExists: true )
+                ])
+                """
+            }
+        }
+        run("METAPHLAN_METAPHLAN") {
+            script "../../../metaphlan/metaphlan/main.nf"
+            process {
+                """
+                input[0] = Channel.of(
+                    [ [ id: 'test', single_end: true], file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',checkIfExists: true ) ],
+                    [ [ id: 'test2', single_end: true], file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz',checkIfExists: true ) ],
+                )
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - illumina single end [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = METAPHLAN_METAPHLAN.out.profile.map{meta, profile -> [[id: 'test'], profile]}.groupTuple()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot( process.out ).match() }
+            )
+        }
+    }
+
+
+    test("sarscov2 - illumina single end [fastq] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = METAPHLAN_METAPHLAN.out.profile.map{meta, profile -> [[id: 'test'], profile]}.groupTuple()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot( process.out ).match() }
+            )
+        }
+    }
+}

modules/nf-core/metaphlan/mergemetaphlantables/tests/main.nf.test.snap

@@ -0,0 +1,68 @@
+{
+    "sarscov2 - illumina single end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4687feab0c102fdc65fe2e174431a7c7"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4687feab0c102fdc65fe2e174431a7c7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-15T07:57:23.888779527"
+    },
+    "sarscov2 - illumina single end [fastq]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,671ac0cf0c2561154fc44109b6d8b973"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4687feab0c102fdc65fe2e174431a7c7"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,671ac0cf0c2561154fc44109b6d8b973"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4687feab0c102fdc65fe2e174431a7c7"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-15T07:53:05.914944433"
+    }
+}

modules/nf-core/metaphlan/mergemetaphlantables/tests/nextflow.config

@@ -0,0 +1,10 @@
+docker {
+    fixOwnership = true
+    runOptions = '--platform=linux/amd64'
+}
+
+process {
+    withName: UNTAR {
+        ext.args2 = "--no-same-owner"
+    }
+}

modules/nf-core/metaphlan/mergemetaphlantables/tests/tags.yml

@@ -0,0 +1,4 @@
+metaphlan/mergemetaphlantables:
+  - "modules/nf-core/metaphlan/mergemetaphlantables/**"
+  - "modules/nf-core/metaphlan/metaphlan/**"
+  - "modules/nf-core/untar/**"

modules/nf-core/metaphlan/metaphlan/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::metaphlan=4.0.6
+  - bioconda::metaphlan=4.1.1

modules/nf-core/metaphlan/metaphlan/main.nf

@@ -4,8 +4,8 @@ process METAPHLAN_METAPHLAN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/metaphlan:4.0.6--pyhca03a8a_0' :
-        'biocontainers/metaphlan:4.0.6--pyhca03a8a_0' }"
+        'https://depot.galaxyproject.org/singularity/metaphlan:4.1.1--pyhdfd78af_0' :
+        'biocontainers/metaphlan:4.1.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)
@@ -47,4 +47,21 @@ process METAPHLAN_METAPHLAN {
         metaphlan: \$(metaphlan --version 2>&1 | awk '{print \$3}')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_type = "$input" =~ /.*\.(fastq|fq)/ ? "--input_type fastq" : "$input" =~ /.*\.(fasta|fna|fa)/ ? "--input_type fasta" : "$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"
+
+    """
+    touch ${prefix}.biom
+    touch ${prefix}_profile.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        metaphlan: \$(metaphlan --version 2>&1 | awk '{print \$3}')
+    END_VERSIONS
+    """
 }

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

@@ -23,7 +23,7 @@ input:
       type: file
       description: Metaphlan 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}"
-  - metaphlan_db:
+  - metaphlan_db_latest:
       type: file
       description: |
         Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/.
@@ -47,7 +47,7 @@ output:
       type: file
       description: General-use format for representing biological sample by observation contingency tables
       pattern: "*.{biom}"
-  - bowtie2out:
+  - bt2out:
       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}"

modules/nf-core/metaphlan/metaphlan/tests/main.nf.test

@@ -0,0 +1,136 @@
+nextflow_process {
+    name "Test Process METAPHLAN_METAPHLAN"
+    script "../main.nf"
+    config "./nextflow.config"
+
+    process "METAPHLAN_METAPHLAN"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untar"
+    tag "metaphlan"
+    tag "metaphlan/metaphlan"
+
+    setup {
+        run("UNTAR") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [],
+                    file( params.modules_testdata_base_path + 'delete_me/metaphlan4_database.tar.gz', checkIfExists: true )
+                ])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - illumina single end [fastq]") {
+
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',checkIfExists: true )
+                ])
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        path(process.out.profile[0][1]).readLines()[2..5],
+                        path(process.out.biom[0][1]).readLines().last().contains('Biological Observation Matrix'),
+                        process.out.bt2out,
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("sarscov2 - illumina pair end [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',checkIfExists: true ),
+                    file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz',checkIfExists: true ) ]
+                ])
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        path(process.out.profile[0][1]).readLines()[2..5],
+                        path(process.out.biom[0][1]).readLines().last().contains('Biological Observation Matrix'),
+                        process.out.bt2out,
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("sarscov2 - illumina single end [fasta]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta',checkIfExists: true )
+                ])
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        path(process.out.profile[0][1]).readLines()[2..5],
+                        path(process.out.biom[0][1]).readLines().last().contains('Biological Observation Matrix'),
+                        process.out.bt2out,
+                        process.out.versions
+                    ).match()
+                }            )
+        }
+    }
+
+    test("sarscov2 - illumina pair end [fastq] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [ file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',checkIfExists: true ),
+                    file( params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz',checkIfExists: true )]
+                ])
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot( process.out ).match() }
+            )
+        }
+    }
+}