Add new module: qcatch

modules/nf-core/qcatch/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::qcatch=0.2.8

modules/nf-core/qcatch/main.nf

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+process QCATCH {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/qcatch:0.2.8--3089b62e628f96d7':
+        'community.wave.seqera.io/library/qcatch:0.2.8--454a9b478b62c36f' }"
+    input:
+    tuple val(meta), val(chemistry), path(quant_dir)
+
+    output:
+    tuple val(meta), path("*.html")                         , emit: report
+    tuple val(meta), path("*_filtered_quants.h5ad") , emit: filtered_h5ad
+    tuple val(meta), path("*_metrics_summary.csv")  , emit: metrics_summary
+    path  "versions.yml"                                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    qcatch \\
+        --input ${quant_dir} \\
+        --output ${prefix} \\
+        --chemistry ${chemistry} \\
+        --save_filtered_h5ad \\
+        --export_summary_table \\
+        ${args}
+
+    mv ${prefix}/QCatch_report.html ${prefix}_qcatch_report.html
+    mv ${prefix}/filtered_quants.h5ad ${prefix}_filtered_quants.h5ad
+    mv ${prefix}/summary_table.csv ${prefix}_metrics_summary.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        qcatch: \$(qcatch --version | sed -e "s/qcatch //g")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}_qcatch_report.html
+    touch ${prefix}_filtered_quants.h5ad
+    touch ${prefix}_metrics_summary.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        qcatch: \$(qcatch --version | sed -e "s/qcatch //g")
+    END_VERSIONS
+    """
+}

modules/nf-core/qcatch/meta.yml

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+name: qcatch
+description: Cell-filtering and QC reporting tool for alevin-fry quantification results
+keywords:
+  - single-cell
+  - quality control
+  - alevin-fry
+  - cell filtering
+  - QC report
+tools:
+  - qcatch:
+      description: |
+        QCatch is a quality control and cell filtering tool designed for single-cell RNA-seq data processed by alevin-fry.
+        It generates comprehensive QC reports and filtered count matrices.
+      homepage: https://github.com/COMBINE-lab/QCatch
+      licence: ["BSD-3-Clause"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - chemistry:
+        type: string
+        description: |
+          Chemistry type for the single-cell experiment, which determines the partition range for the empty_drops step.
+          Supported values: '10X_3p_v2', '10X_3p_v3', '10X_3p_v4', '10X_5p_v3', '10X_3p_LT', '10X_HT'.
+          If using a standard 10X chemistry and quantification was performed with simpleaf (v0.19.5 or later),
+          QCatch will try to infer the correct chemistry from the metadata.
+    - quant_dir:
+        type: directory
+        description: |
+          Directory containing alevin-fry quantification results (af_quant output from simpleaf quant).
+          Must contain the quantification matrix and associated metadata files.
+        ontologies: []
+output:
+  report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: |
+            HTML QC report generated by QCatch containing visualizations and metrics
+          pattern: "*.html"
+          ontologies: []
+  filtered_h5ad:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_filtered_quants.h5ad":
+          type: file
+          description: |
+            Filtered quantification matrix in h5ad format (AnnData)
+          pattern: "*_filtered_quants.h5ad"
+          ontologies: []
+  metrics_summary:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_metrics_summary.csv":
+          type: file
+          description: |
+            CSV file containing summary metrics from QC analysis
+          pattern: "*_metrics_summary.csv"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: |
+          File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@wzheng0520"
+  - "@dongzehe"
+maintainers:
+  - "@wzheng0520"
+  - "@dongzehe"

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

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+nextflow_process {
+
+    name "Test Process QCATCH"
+    script "../main.nf"
+    process "QCATCH"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "qcatch"
+    tag "unzip"
+
+    test("test_qcatch - 1k_pbmc_v3") {
+
+        setup {
+            // Download and extract QCatch test data from COMBINE-lab using UNZIP module
+            run("UNZIP") {
+                script "modules/nf-core/unzip/main.nf"
+                process {
+                    """
+                    meta = [id:'qcatch_test_data']
+                    input[0] = Channel.of([meta, file('https://umd.box.com/shared/static/zd4sai70uw9fs24e1qx6r41ec50pf45g.zip')])
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                // Get the 1k_pbmc_v3 subdirectory from the extracted archive
+                input[0] = UNZIP.out.unzipped_archive.map { meta, dir ->
+                    def quant_dir = file("\${dir}/test_data/1k_pbmc_v3")
+                    [[id:'1k_pbmc_v3'], '10X_3p_v3', quant_dir]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.report.get(0).get(1)).exists() },
+                { assert file(process.out.filtered_h5ad.get(0).get(1)).exists() },
+                { assert file(process.out.metrics_summary.get(0).get(1)).exists() },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+
+    test("test_qcatch - stub") {
+        options "-stub-run"
+
+        when {
+            process {
+                """
+                meta = [id:'test_stub']
+                input[0] = Channel.of([meta, '10X_3p_v3', file('stub_quant_dir')])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

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

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+{
+    "test_qcatch - 1k_pbmc_v3": {
+        "content": [
+            [
+                "versions.yml:md5,46f73aa6be1b23a13365040ab92e22af"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
+        },
+        "timestamp": "2026-02-13T21:36:15.677759721"
+    },
+    "test_qcatch - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_qcatch_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_filtered_quants.h5ad:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_metrics_summary.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,46f73aa6be1b23a13365040ab92e22af"
+                ],
+                "filtered_h5ad": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_filtered_quants.h5ad:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "metrics_summary": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_metrics_summary.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub_qcatch_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,46f73aa6be1b23a13365040ab92e22af"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-02-13T21:56:57.673052701"
+    }
+}

modules/nf-core/qcatch/tests/nextflow.config

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+env {
+    MPLCONFIGDIR        = "./tmp"
+    NUMBA_CACHE_DIR     = "./tmp"
+    NUMBA_DISABLE_CACHE = 1
+}