Added pbtk/pbindex (#5901)

* Added pbtk/pbindex

* Removed prefix

modules/nf-core/pbtk/pbindex/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "pbtk_pbindex"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::pbtk=3.1.1"

modules/nf-core/pbtk/pbindex/main.nf

@@ -0,0 +1,41 @@
+process PBTK_PBINDEX {
+    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/pbtk:3.1.1--h9ee0642_0':
+        'biocontainers/pbtk:3.1.1--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.pbi"), emit: pbi
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    pbindex \\
+        -j $task.cpus \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbindex: \$(pbindex --version | sed -n 's/pbindex \\(.*\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${bam}.pbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbindex: \$(pbindex --version | sed -n 's/pbindex \\(.*\\)/\\1/p')
+    END_VERSIONS
+    """
+}

modules/nf-core/pbtk/pbindex/meta.yml

@@ -0,0 +1,48 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pbtk_pbindex"
+description: Minimalistic tool which creates an index file that enables random access into PacBio BAM files
+keywords:
+  - genomics
+  - bam
+  - index
+  - pacbio
+tools:
+  - "pbtk":
+      description: "pbtk - PacBio BAM toolkit"
+      homepage: "https://github.com/PacificBiosciences/pbtk"
+      documentation: "https://github.com/PacificBiosciences/pbtk"
+      tool_dev_url: "https://github.com/PacificBiosciences/pbtk"
+      licence: ["BSD-3-clause-Clear"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - bam:
+      type: file
+      description: Input BAM file
+      pattern: "*.bam"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - pbi:
+      type: file
+      description: Index file
+      pattern: "*.bam.pbi"
+
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"

modules/nf-core/pbtk/pbindex/tests/main.nf.test

@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process PBTK_PBINDEX"
+    script "../main.nf"
+    process "PBTK_PBINDEX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pbtk"
+    tag "pbtk/pbindex"
+
+    test("homo_sapiens - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/pbtk/pbindex/tests/main.nf.test.snap

@@ -0,0 +1,68 @@
+{
+    "homo_sapiens - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "alz.bam.pbi:md5,085d6c04da9daa5f984767b158a879f4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a162e157c7ce09585c86cb390d00f94e"
+                ],
+                "pbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "alz.bam.pbi:md5,085d6c04da9daa5f984767b158a879f4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a162e157c7ce09585c86cb390d00f94e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T12:16:24.358838"
+    },
+    "homo_sapiens - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "alz.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a162e157c7ce09585c86cb390d00f94e"
+                ],
+                "pbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "alz.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a162e157c7ce09585c86cb390d00f94e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T12:16:29.083998"
+    }
+}