New module: COPTR/EXTRACT

modules/nf-core/coptr/extract/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::coptr=1.1.4"

modules/nf-core/coptr/extract/main.nf

@@ -0,0 +1,48 @@
+process COPTR_EXTRACT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/coptr:1.1.4--pyhdfd78af_3':
+        'biocontainers/coptr:1.1.4--pyhdfd78af_3' }"
+
+    input:
+    tuple val(meta), path(bam, stageAs: "bamfolder/*")
+
+    output:
+    tuple val(meta), path("*.pkl"), emit: coverage
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    coptr \\
+        extract \\
+        $args \\
+        bamfolder/ \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.pkl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        "${task.process}":
+            coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
+    END_VERSIONS
+    """
+}

modules/nf-core/coptr/extract/meta.yml

@@ -0,0 +1,56 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "coptr_extract"
+description: Computes the coverage map along the reference genome
+keywords:
+  - coptr
+  - mapping
+  - ptr
+tools:
+  - "coptr":
+      description: "Accurate and robust inference of microbial growth dynamics from
+        metagenomic sequencing reads."
+      homepage: "https://github.com/tyjo/coptr"
+      documentation: "https://coptr.readthedocs.io/"
+      tool_dev_url: "https://github.com/tyjo/coptr"
+      doi: "10.1101/gr.275533.121"
+      licence: ["GPL v3"]
+      identifier: biotools:coptr
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: bam file with the mapping of the reads on the reference genome
+        pattern: "*.{.bam}"
+        ontologies:
+            - edam: "http://edamontology.org/format_2572"
+
+output:
+  - coverage:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.pkl":
+          type: file
+          description: Python pickle (pkl) file containing coverage along the reference genome
+          pattern: "*.{pkl}"
+          ontologies:
+            - edam: "http://edamontology.org/format_4002"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@ramirobarrantes"
+maintainers:
+  - "@ramirobarrantes"

modules/nf-core/coptr/extract/tests/main.nf.test

@@ -0,0 +1,86 @@
+nextflow_process {
+
+    name "Test Process COPTR_EXTRACT"
+    script "../main.nf"
+    process "COPTR_EXTRACT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "coptr"
+    tag "coptr/extract"
+
+
+    test("coptr extract single bam file") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'indexNameExample'],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+                }
+            )
+        }
+
+    }
+
+    test("coptr extract two bam files") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'indexNameExample'],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+                }
+            )
+        }
+    }
+
+    test("coptr extract single bam file - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'indexNameExample'],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+                }
+            )
+        }
+
+    }
+}

modules/nf-core/coptr/extract/tests/main.nf.test.snap

@@ -0,0 +1,107 @@
+{
+    "coptr extract two bam files": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "indexNameExample"
+                        },
+                        [
+                            "test.paired_end.sorted.cm.pkl:md5,c60bb7cb7cba50898c95b2406516ec5f",
+                            "test.single_end.cm.pkl:md5,128ae12d6548a0640ddace5fc7a7eea8"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c6fcaf8fb6aa9c10a3192d81f9623d4f"
+                ],
+                "coverage": [
+                    [
+                        {
+                            "id": "indexNameExample"
+                        },
+                        [
+                            "test.paired_end.sorted.cm.pkl:md5,c60bb7cb7cba50898c95b2406516ec5f",
+                            "test.single_end.cm.pkl:md5,128ae12d6548a0640ddace5fc7a7eea8"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c6fcaf8fb6aa9c10a3192d81f9623d4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-25T16:06:26.239512"
+    },
+    "coptr extract single bam file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "indexNameExample"
+                        },
+                        "test.paired_end.sorted.cm.pkl:md5,c60bb7cb7cba50898c95b2406516ec5f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,c6fcaf8fb6aa9c10a3192d81f9623d4f"
+                ],
+                "coverage": [
+                    [
+                        {
+                            "id": "indexNameExample"
+                        },
+                        "test.paired_end.sorted.cm.pkl:md5,c60bb7cb7cba50898c95b2406516ec5f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c6fcaf8fb6aa9c10a3192d81f9623d4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-25T16:04:59.852647"
+    },
+    "coptr extract single bam file - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "indexNameExample"
+                        },
+                        "indexNameExample.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,578f185b99f7f5ba27eb2a9f44c1d6a9"
+                ],
+                "coverage": [
+                    [
+                        {
+                            "id": "indexNameExample"
+                        },
+                        "indexNameExample.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,578f185b99f7f5ba27eb2a9f44c1d6a9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-02T19:26:21.856688"
+    }
+}