pbsv (nf-core#6818)

* pbsv * [automated] Fix linting with Prettier * version of pbsv module where all the tests pass * getting rid of un-need comments * updated: * changed website: * update * deleting accidental file * small tweak * updating the meta description * pretty * removing trailing space * space * newline * should pass version test * changed pbsv to pbsv/discover - seperating functionality * Update modules/nf-core/pbsv/discover/tests/main.nf.test Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/pbsv/discover/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/pbsv/discover/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update modules/nf-core/pbsv/discover/meta.yml Co-authored-by: Felix Lenner <[email protected]> * resolving comments * resolving comments * comments --------- Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Felix Lenner <[email protected]>
LouisLeNezet · Oct 31, 2024 · 6c32d37 · 6c32d37
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diff --git a/modules/nf-core/pbsv/discover/environment.yml b/modules/nf-core/pbsv/discover/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::pbsv=2.9.0"
diff --git a/modules/nf-core/pbsv/discover/main.nf b/modules/nf-core/pbsv/discover/main.nf
@@ -0,0 +1,46 @@
+process PBSV_DISCOVER {
+    tag "$meta.id"
+    label 'process_single'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0':
+        'biocontainers/pbsv:2.9.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(fasta)
+
+    output:
+    tuple val(meta), path("*.svsig.gz"), emit: svsig
+    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}"
+    """
+    pbsv \\
+        discover \\
+        $args \\
+        ${bam} \\
+        ${prefix}.svsig.gz
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo | gzip > ${prefix}.svsig.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/pbsv/discover/meta.yml b/modules/nf-core/pbsv/discover/meta.yml
@@ -0,0 +1,54 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pbsv_discover"
+description: "pbsv - PacBio structural variant (SV) signature discovery tool"
+keywords:
+  - variant
+  - pacbio
+  - structural
+tools:
+  - "pbsv":
+      description: "pbsv - PacBio structural variant (SV) calling and analysis tools"
+      homepage: "https://github.com/PacificBiosciences/pbsv"
+      documentation: "https://github.com/PacificBiosciences/pbsv"
+      tool_dev_url: "https://github.com/PacificBiosciences/pbsv"
+      licence: ["BSD-3-clause-Clear"]
+      identifier: ""
+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 reference information
+          e.g. `[ id:'reference' ]`
+    - fasta:
+        type: file
+        description: fasta file
+        pattern: "*.fasta"
+output:
+  - svsig:
+      - meta:
+          type: file
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.svsig.gz":
+          type: file
+          description: structural variant signatures files
+          pattern: "*.svsig.gz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@tanyasarkjain"
+maintainers:
+  - "@tanyasarkjain"
diff --git a/modules/nf-core/pbsv/discover/tests/main.nf.test b/modules/nf-core/pbsv/discover/tests/main.nf.test
@@ -0,0 +1,65 @@
+nextflow_process {
+
+    name "Test Process PBSV_DISCOVER"
+    script "../main.nf"
+    process "PBSV_DISCOVER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pbsv"
+    tag "pbsv/discover"
+
+    test("pbsv_bam") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path +  'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true)
+                ]
+
+                input[1] = [
+                    [ id:'test', single_end:false ], // 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("pbsv_bam_stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path +  'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test', single_end:false ], // 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() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/pbsv/discover/tests/main.nf.test.snap b/modules/nf-core/pbsv/discover/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "pbsv_bam_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.svsig.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a"
+                ],
+                "svsig": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.svsig.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T11:24:59.172558"
+    },
+    "pbsv_bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.svsig.gz:md5,7c4859b65e51d8d2c9ab1e5338da17c1"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a"
+                ],
+                "svsig": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.svsig.gz:md5,7c4859b65e51d8d2c9ab1e5338da17c1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-30T11:24:46.288774"
+    }
+}