WIP: New Module: Pychopper (#7438)

* WIP- add pychopper

* meta yml complete

* Test and snap

* Add stub gzipped format, working version

* try remove all blank entries in meta yml

* linted

* Update main.nf

add version as def var

modules/nf-core/pychopper/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::pychopper=2.7.10"

modules/nf-core/pychopper/main.nf

@@ -0,0 +1,52 @@
+process PYCHOPPER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pychopper:2.7.10--pyhdfd78af_0':
+        'biocontainers/pychopper:2.7.10--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.out.fastq.gz"), emit: fastq
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def PYCHOPPER_VERSION = '2.7.10'
+
+    """
+    pychopper \\
+        $args \\
+        -t $task.cpus \\
+        $fastq \\
+        ${prefix}.out.fastq
+
+    gzip -f ${prefix}.out.fastq > ${prefix}.out.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pychopper: $PYCHOPPER_VERSION (hard coded- check container used for this module)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.out.fastq
+    gzip ${prefix}.out.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pychopper: 2.7.10 (hard coded- check container used for this module)
+    END_VERSIONS
+    """
+}

modules/nf-core/pychopper/meta.yml

@@ -0,0 +1,54 @@
+name: "pychopper"
+description: Identify, orient and trim nanopore cDNA reads
+keywords:
+  - sort
+  - trimming
+  - nanopore
+tools:
+  - "pychopper":
+      description: "A tool to identify, orient and rescue full length cDNA reads from
+        nanopore data."
+      homepage: "https://github.com/epi2me-labs/pychopper"
+      documentation: "https://github.com/epi2me-labs/pychopper"
+      tool_dev_url: "https://github.com/epi2me-labs/pychopper"
+      licence: ["Oxford Nanopore Technologies PLC. Public License Version 1.0"]
+      identifier: ""
+  - "gzip":
+      description: "Gzip reduces the size of the named files using Lempel-Ziv coding
+        (LZ77)."
+      documentation: "https://linux.die.net/man/1/gzip"
+      args_id: "$args3"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fastq:
+        type: file
+        description: FastQ with reads from long read sequencing e.g. nanopore
+        pattern: "*.{fastq.gz}"
+output:
+  - fastq:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{fastq.gz}"
+      - "*.out.fastq.gz":
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+          pattern: "*.{fastq.gz}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@chriswyatt1"
+maintainers:
+  - "@chriswyatt1"

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

@@ -0,0 +1,69 @@
+nextflow_process {
+
+    name "Test Process PYCHOPPER"
+    script "../main.nf"
+    process "PYCHOPPER"
+    tag "pychopper"
+    tag "modules"
+    tag "modules_nfcore"
+
+    test("pychopper-test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] =  [
+                                [id:'test_out' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+
+            def fastq_content = path(process.out.fastq.get(0).get(1)).linesGzip
+
+            assertAll(
+                { assert process.success },
+                // original pytest checks
+                { assert process.out.fastq.get(0).get(1) ==~ ".*/test_out.out.fastq.gz" },
+                // additional nf-test checks
+                // Order of reads is not deterministic, so only assess whether the number of reads is correct
+                { assert snapshot(
+                    process.out.fastq,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("test-pychopper-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] =  [
+                                [id:'test_out' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.fastq,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,42 @@
+{
+    "pychopper-test": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_out"
+                    },
+                    "test_out.out.fastq.gz:md5,04f3003f5cb5a78d90cae351beacb094"
+                ]
+            ],
+            [
+                "versions.yml:md5,1431ed95e3c77f8742c7b014b26e50f5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-05T13:57:08.581810556"
+    },
+    "test-pychopper-stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_out"
+                    },
+                    "test_out.out.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,1431ed95e3c77f8742c7b014b26e50f5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-05T15:09:38.47491875"
+    }
+}