nf-core-module-dev claude init attempt for hifiadapterfilt

modules/nf-core/hifiadapterfilt/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/hifiadapterfilt
+  - bioconda::hifiadapterfilt=3.0.0

modules/nf-core/hifiadapterfilt/main.nf

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+process HIFIADAPTERFILT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hifiadapterfilt:3.0.0--hdfd78af_0':
+        'quay.io/biocontainers/hifiadapterfilt:3.0.0--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("${prefix}.filt.fastq.gz")       , emit: fastq
+    tuple val(meta), path("${prefix}.stats")               , emit: stats
+    tuple val(meta), path("${prefix}.contaminant.blastout"), emit: blastout
+    tuple val(meta), path("${prefix}.blocklist")           , emit: blocklist
+    tuple val("${task.process}"), val('hifiadapterfilt'), eval("hifiadapterfilt.sh --version 2>&1 | head -1"), topic: versions, emit: versions_hifiadapterfilt
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    ln -s \$(realpath ${bam}) ${prefix}.bam
+
+    hifiadapterfilt.sh \\
+        -t ${task.cpus} \\
+        -o . \\
+        ${args}
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.filt.fastq.gz
+    touch ${prefix}.stats
+    touch ${prefix}.contaminant.blastout
+    touch ${prefix}.blocklist
+    """
+}

modules/nf-core/hifiadapterfilt/meta.yml

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+name: hifiadapterfilt
+description: |
+  Remove adapter sequences from PacBio HiFi (CCS) reads using BLAST-based
+  detection. Produces filtered FASTQ output, filtering statistics, BLAST hits,
+  and a list of blocked read IDs.
+keywords:
+  - pacbio
+  - hifi
+  - adapter
+  - filtering
+  - long reads
+  - ccs
+tools:
+  - hifiadapterfilt:
+      description: |
+        HiFiAdapterFilt uses BLAST to identify and remove adapter sequences
+        from PacBio HiFi reads, producing adapter-filtered FASTQ output along
+        with detailed statistics.
+      homepage: https://github.com/sheinasim/HiFiAdapterFilt
+      documentation: https://github.com/sheinasim/HiFiAdapterFilt
+      tool_dev_url: https://github.com/sheinasim/HiFiAdapterFilt
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bam:
+        type: file
+        description: PacBio HiFi reads in BAM format
+        pattern: "*.bam"
+        ontologies: []
+output:
+  fastq:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}.filt.fastq.gz:
+          type: file
+          description: Adapter-filtered reads in gzipped FASTQ format
+          pattern: "*.filt.fastq.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_1930 # FASTQ
+  stats:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}.stats:
+          type: file
+          description: Filtering statistics file
+          pattern: "*.stats"
+          ontologies:
+            - edam: http://edamontology.org/format_3671 # Plain text
+  blastout:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}.contaminant.blastout:
+          type: file
+          description: BLAST tabular output for reads containing adapter sequences
+          pattern: "*.contaminant.blastout"
+          ontologies: []
+  blocklist:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}.blocklist:
+          type: file
+          description: List of read IDs blocked due to adapter contamination
+          pattern: "*.blocklist"
+          ontologies:
+            - edam: http://edamontology.org/format_3671 # Plain text
+  versions_hifiadapterfilt:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hifiadapterfilt:
+          type: string
+          description: The name of the tool
+      - hifiadapterfilt.sh --version 2>&1 | head -1:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hifiadapterfilt:
+          type: string
+          description: The name of the tool
+      - hifiadapterfilt.sh --version 2>&1 | head -1:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@vagkaratzas"
+maintainers:
+  - "@vagkaratzas"

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

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+nextflow_process {
+
+    name "Test Process HIFIADAPTERFILT"
+    script "../main.nf"
+    process "HIFIADAPTERFILT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hifiadapterfilt"
+
+    test("homo_sapiens - pacbio ccs bam - fastq") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.bam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.fastq,
+                    path(process.out.blastout[0][1]).exists(),
+                    path(process.out.blocklist[0][1]).exists(),
+                    path(process.out.stats[0][1]).exists(),
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - pacbio ccs bam - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.bam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}

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

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+{
+    "homo_sapiens - pacbio ccs bam - fastq": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.filt.fastq.gz:md5,ce026e6b05113c474da0ef6570fbb04c"
+                ]
+            ],
+            true,
+            true,
+            true,
+            {
+                "versions_hifiadapterfilt": [
+                    [
+                        "HIFIADAPTERFILT",
+                        "hifiadapterfilt",
+                        "3.0.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-04-25T10:08:26.23596593"
+    },
+    "homo_sapiens - pacbio ccs bam - fastq - stub": {
+        "content": [
+            {
+                "blastout": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contaminant.blastout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "blocklist": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.blocklist:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filt.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_hifiadapterfilt": [
+                    [
+                        "HIFIADAPTERFILT",
+                        "hifiadapterfilt",
+                        "3.0.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-04-25T10:08:33.302793639"
+    }
+}