New module: hashsolo

modules/nf-core/scanpy/hashsolo/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::python=3.12.11
+  - conda-forge::pyyaml=6.0.2
+  - conda-forge::scanpy=1.11.2

modules/nf-core/scanpy/hashsolo/main.nf

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+process SCANPY_HASHSOLO {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/16/168ecbbe27ccef766741ccbf937b0d2675be2e19b0565035e0719f1e9ea5ee95/data':
+        'community.wave.seqera.io/library/python_pyyaml_scanpy:b5509a698e9aae25' }"
+
+    input:
+    tuple val(meta), path(input_h5ad), val(cell_hashing_columns)
+
+    output:
+    tuple val(meta), path("*.h5ad"), emit: h5ad
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    priors = task.ext.priors ?: '0.01,0.8,0.19'
+    template('hashsolo.py')
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.h5ad
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python3 --version | cut -f 2 -d " ")
+        scanpy: \$(python3 -c "import scanpy; print(scanpy.__version__)")
+    END_VERSIONS
+    """
+}

modules/nf-core/scanpy/hashsolo/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "SCANPY_HASHSOLO"
+description: Probabilistic demultiplexing of cell hashing data
+keywords:
+  - anndata
+  - single-cell
+  - hashing
+  - demultiplexing
+  - scanpy
+tools:
+  - "scanpy":
+      description: "Single-cell analysis in Python. Scales to >100M cells."
+      homepage: "https://github.com/scverse/scanpy"
+      documentation: "https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.hashsolo.html"
+      tool_dev_url: "https://github.com/scverse/scanpy"
+      doi: "10.1186/s13059-017-1382-0"
+      licence: ["BSD-3"]
+      identifier: biotools:scanpy
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - input_h5ad:
+        type: file
+        description: The (annotated) data matrix of shape n_obs x n_vars. Rows
+          correspond to cells and columns to genes.
+        pattern: "*.h5ad"
+        ontologies: []
+    - cell_hashing_columns:
+        type: list
+        description: |
+          List of cell hashing columns to use for demultiplexing.
+          e.g. `['hash_1', 'hash_2']`
+
+output:
+  - h5ad:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+          pattern: "*.h5ad"
+      - "*.h5ad":
+          type: file
+          description: |
+            AnnData file containing cluster feature, etc.
+          pattern: "*.h5ad"
+          ontologies: []
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@seohyonkim"
+maintainers:
+  - "@seohyonkim"

modules/nf-core/scanpy/hashsolo/templates/hashsolo.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+
+import os
+import platform
+import yaml
+
+os.environ["MPLCONFIGDIR"] = "./tmp/mpl"
+os.environ["NUMBA_CACHE_DIR"] = "./tmp/numba"
+
+import scanpy as sc
+import scanpy.external as sce
+
+
+adata = sc.read_h5ad("${input_h5ad}")
+columns = "${cell_hashing_columns.join(' ')}".split()
+columns_str = [str(x) for x in columns]
+sce.pp.hashsolo(adata, columns_str, priors=[float(prior) for prior in "${priors}".split(',')])
+
+adata.write("${prefix}.h5ad")
+
+versions = {
+    "${task.process}": {
+        "python": platform.python_version(),
+        "scanpy": sc.__version__,
+    }
+}
+
+with open("versions.yml", "w") as f:
+    yaml.dump(versions, f)

modules/nf-core/scanpy/hashsolo/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process SCANPY_HASHSOLO"
+    script "../main.nf"
+    process "SCANPY_HASHSOLO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hashsolo"
+    tag "scanpy/hashsolo"
+    tag "scanpy"
+
+    test("generated h5ad") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/hashsolo_anndata.h5ad', checkIfExists: true),
+                    ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("generated h5ad - stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/hashsolo_anndata.h5ad', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/scanpy/hashsolo/tests/main.nf.test.snap

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+{
+    "generated h5ad": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_hashsolo.h5ad:md5,e1f129270b67e8575dd060d44e1c0c4b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d4b55c68ad8effa4580cf202d802b007"
+                ],
+                "h5ad": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_hashsolo.h5ad:md5,e1f129270b67e8575dd060d44e1c0c4b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d4b55c68ad8effa4580cf202d802b007"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.3"
+        },
+        "timestamp": "2025-06-15T16:12:56.470744429"
+    },
+    "generated h5ad - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_hashsolo.h5ad:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,59133af84f960e142d89d672f0c32cff"
+                ],
+                "h5ad": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_hashsolo.h5ad:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,59133af84f960e142d89d672f0c32cff"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.3"
+        },
+        "timestamp": "2025-06-15T16:21:51.26475278"
+    }
+}

modules/nf-core/scanpy/hashsolo/tests/nextflow.config

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+process {
+    withName: SCANPY_HASHSOLO {
+        ext.prefix = { "${meta.id}_hashsolo"}
+    }
+}