[Won't merge] Codex checkpoint - to compare against Claude

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:
+  - bioconda::hifiadapterfilt=3.0.0

modules/nf-core/hifiadapterfilt/main.nf

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+process HIFIADAPTERFILT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hifiadapterfilt:3.0.0--hdfd78af_0':
+        'quay.io/biocontainers/hifiadapterfilt:3.0.0--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("${prefix}.contaminant.blastout"), emit: blastout
+    tuple val(meta), path("${prefix}.blocklist")            , emit: blocklist
+    tuple val(meta), path("${prefix}.filt.fastq.gz")        , emit: fastq
+    tuple val(meta), path("${prefix}.stats")                , emit: stats
+    tuple val("${task.process}"), val('hifiadapterfilt'), eval('echo 3.0.0'), topic: versions, emit: versions_hifiadapterfilt
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    def input_ext = "$reads".endsWith('.fastq.gz') ? '.fastq.gz' :
+        "$reads".endsWith('.fq.gz')                ? '.fq.gz' :
+        "$reads".endsWith('.fastq')                ? '.fastq' :
+        "$reads".endsWith('.fq')                   ? '.fq' :
+        "$reads".endsWith('.bam')                  ? '.bam' :
+        error("Unsupported input file extension for HiFiAdapterFilt: ${reads}")
+    def tool_prefix = "hifiadapterfilt_input"
+    """
+    mkdir -p hifiadapterfilt_work
+    ln -sf "../${reads}" "hifiadapterfilt_work/${tool_prefix}${input_ext}"
+
+    (
+        cd hifiadapterfilt_work
+        hifiadapterfilt.sh \\
+            -p all \\
+            -t ${task.cpus} \\
+            -o .. \\
+            ${args}
+    )
+
+    if [[ "${tool_prefix}" != "${prefix}" ]]; then
+        mv ${tool_prefix}.contaminant.blastout ${prefix}.contaminant.blastout
+        mv ${tool_prefix}.blocklist ${prefix}.blocklist
+        mv ${tool_prefix}.filt.fastq.gz ${prefix}.filt.fastq.gz
+        mv ${tool_prefix}.stats ${prefix}.stats
+    fi
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.contaminant.blastout
+    touch ${prefix}.blocklist
+    echo "" | gzip > ${prefix}.filt.fastq.gz
+    touch ${prefix}.stats
+    """
+}

modules/nf-core/hifiadapterfilt/meta.yml

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+name: hifiadapterfilt
+description: Remove remnant PacBio adapter sequences from HiFi reads and convert BAM input to compressed FASTQ
+keywords:
+  - PacBio
+  - HiFi
+  - adapter filtering
+  - long reads
+  - FASTQ
+tools:
+  - hifiadapterfilt:
+      description: HiFiAdapterFilt removes CCS reads with remnant PacBio adapter sequences and converts outputs to compressed FASTQ.
+      homepage: https://github.com/sheinasim-USDA/HiFiAdapterFilt
+      documentation: https://github.com/sheinasim-USDA/HiFiAdapterFilt
+      tool_dev_url: https://github.com/sheinasim-USDA/HiFiAdapterFilt
+      doi: "10.1186/s12864-022-08375-1"
+      licence:
+        - "GPL-3.0-or-later"
+      identifier: biotools:hifiadapterfilt
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:true ]
+    - reads:
+        type: file
+        description: PacBio HiFi reads in BAM, FASTQ, or gzip-compressed FASTQ format
+        pattern: "*.{bam,fastq,fq,fastq.gz,fq.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_2572 # BAM
+          - edam: http://edamontology.org/format_1930 # FASTQ
+          - edam: http://edamontology.org/format_3989 # GZIP format
+output:
+  blastout:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:true ]
+      - ${prefix}.contaminant.blastout:
+          type: file
+          description: Tabular BLAST output containing reads aligned to PacBio adapter sequences
+          pattern: "*.contaminant.blastout"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  blocklist:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:true ]
+      - ${prefix}.blocklist:
+          type: file
+          description: List of read headers identified as PacBio adapter-contaminated and removed
+          pattern: "*.blocklist"
+          ontologies:
+            - edam: http://edamontology.org/format_2330 # Textual format
+  fastq:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:true ]
+      - ${prefix}.filt.fastq.gz:
+          type: file
+          description: Gzipped FASTQ file containing reads without detected PacBio adapter contamination
+          pattern: "*.filt.fastq.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_1930 # FASTQ
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  stats:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:true ]
+      - ${prefix}.stats:
+          type: file
+          description: Text summary of read counts and adapter-contaminated reads removed
+          pattern: "*.stats"
+          ontologies:
+            - edam: http://edamontology.org/format_2330 # Textual format
+  versions_hifiadapterfilt:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - hifiadapterfilt:
+          type: string
+          description: The tool name
+      - echo 3.0.0:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - hifiadapterfilt:
+          type: string
+          description: The tool name
+      - echo 3.0.0:
+          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 fastq.gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.stats.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.blastout,
+                    process.out.blocklist,
+                    process.out.fastq,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - pacbio fastq.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz', 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 fastq.gz - 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",
+                        "3.0.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-04-25T09:25:43.311147037"
+    },
+    "homo_sapiens - pacbio fastq.gz": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.contaminant.blastout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.blocklist:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.filt.fastq.gz:md5,23a6d8f301d0fd4d2da21f86ff0afac6"
+                ]
+            ],
+            {
+                "versions_hifiadapterfilt": [
+                    [
+                        "HIFIADAPTERFILT",
+                        "hifiadapterfilt",
+                        "3.0.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-04-25T09:38:42.6537421"
+    }
+}