Merge branch 'master' into 325-mixed-model-in-limma

modules/nf-core/pbmm2/align/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::pbmm2=1.14.99"

modules/nf-core/pbmm2/align/main.nf

@@ -0,0 +1,51 @@
+process PBMM2_ALIGN {
+    tag "$meta.id"
+    label 'process_large'
+
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pbmm2:1.14.99--h9ee0642_0':
+        'biocontainers/pbmm2:1.14.99--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(fasta)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    pbmm2 \\
+        align \\
+        $args \\
+        $fasta \\
+        $bam \\
+        ${prefix}.bam \\
+        --num-threads ${task.cpus}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbmm2: \$(pbmm2 --version |& sed '1!d ; s/pbmm2 //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbmm2: \$(pbmm2 --version |& sed '1!d ; s/pbmm2 //')
+    END_VERSIONS
+    """
+}

modules/nf-core/pbmm2/align/meta.yml

@@ -0,0 +1,61 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pbmm2_align"
+description: Alignment with PacBio's minimap2 frontend
+keywords:
+  - align
+  - pacbio
+  - genomics
+tools:
+  - "pbmm2":
+      description: "A minimap2 frontend for PacBio native data formats"
+      homepage: "https://github.com/PacificBiosciences/pbmm2"
+      documentation: "https://github.com/PacificBiosciences/pbmm2"
+      tool_dev_url: "https://github.com/PacificBiosciences/pbmm2"
+      licence: ["BSD-3-clause-Clear"]
+      identifier: biotools:pbmm2
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fasta:
+        type: file
+        description: fasta file to align bam to
+        pattern: "*.{fasta}"
+output:
+  - bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.bam":
+          type: file
+          description: Sorted BAM/CRAM/SAM file
+          pattern: "*.{bam,cram,sam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572"
+            - edam: "http://edamontology.org/format_2573"
+            - edam: "http://edamontology.org/format_3462"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@tanyasarkjain"
+maintainers:
+  - "@tanyasarkjain"

modules/nf-core/pbmm2/align/tests/main.nf.test

@@ -0,0 +1,67 @@
+nextflow_process {
+
+    name "Test Process PBMM2_ALIGN"
+    script "../main.nf"
+    process "PBMM2_ALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pbmm2"
+    tag "pbmm2/align"
+
+    test("pbmm2 - bam") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("pbmm2  - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/pbmm2/align/tests/main.nf.test.snap

@@ -0,0 +1,68 @@
+{
+    "pbmm2 - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,b1d6b50f20ba0389435c6a51de26d836"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e8aa0696ac2bf135b5f88e6cb7e7b18a"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,b1d6b50f20ba0389435c6a51de26d836"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e8aa0696ac2bf135b5f88e6cb7e7b18a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T10:53:18.838135"
+    },
+    "pbmm2  - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e8aa0696ac2bf135b5f88e6cb7e7b18a"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e8aa0696ac2bf135b5f88e6cb7e7b18a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T10:53:31.992125"
+    }
+}