added module 10xbamtofastq

modules/nf-core/bamtofastq10x/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "bamtofastq10x"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::10x_bamtofastq=1.4.1"

modules/nf-core/bamtofastq10x/main.nf

@@ -0,0 +1,45 @@
+process BAMTOFASTQ10X {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/10x_bamtofastq:1.4.1--hdbdd923_2':
+        'biocontainers/10x_bamtofastq:1.4.1--hdbdd923_2' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: fastq
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bamtofastq \\
+        $args \\
+        $bam \\
+        ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtofastq10x: \$(bamtofastq --version |& sed '1!d ; s/bamtofastq //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtofastq10x: \$(bamtofastq --version |& sed '1!d ; s/bamtofastq //')
+    END_VERSIONS
+    """
+}

modules/nf-core/bamtofastq10x/meta.yml

@@ -0,0 +1,48 @@
+name: bamtofastq10x
+
+description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis
+
+keywords:
+  - bam
+  - convert
+  - fastq
+  - 10x
+
+tools:
+  - bamtofastq10x:
+      description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis
+      homepage: https://github.com/10XGenomics/bamtofastq
+      documentation: https://github.com/10XGenomics/bamtofastq
+      tool_dev_url: https://github.com/10XGenomics/bamtofastq
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - bam:
+      type: file
+      description: 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"
+
+  - fastq:
+      type: file
+      description: fastq compressed file
+      pattern: "*.fastq.gz"
+
+authors:
+  - "@BlueBicycleBlog"
+maintainers:
+  - "@BlueBicycleBlog"

modules/nf-core/bamtofastq10x/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process BAMTOFASTQ10X"
+    script "../main.nf"
+    process "BAMTOFASTQ10X"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bamtofastq10x"
+
+    test("human - bam") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/10x_cr12.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+
+            )
+        }
+    }
+
+
+    test("human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/10x_cr12.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+
+    }
+}

modules/nf-core/bamtofastq10x/tests/main.nf.test.snap

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+{
+    "human - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
+                            ]
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,845cd1d09c8a3d0059da9d074a9e5436"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
+                            ]
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,845cd1d09c8a3d0059da9d074a9e5436"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.0"
+        },
+        "timestamp": "2024-05-22T16:43:24.999397"
+    }
+}

modules/nf-core/bamtofastq10x/tests/tags.yml

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+bamtofastq10x:
+  - "modules/nf-core/bamtofastq10x/**"