New module: anndata/getsize module

modules/nf-core/anndata/getsize/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::anndata=0.10.9

modules/nf-core/anndata/getsize/main.nf

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+process ANNDATA_GETSIZE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/anndata:0.10.9--d13580e4b297da7c':
+        'community.wave.seqera.io/library/anndata:0.10.9--1eab54e300e1e584' }"
+
+    input:
+    tuple val(meta), path(h5ad)
+    val size_type
+
+    output:
+    tuple val(meta), path("*.txt"), emit: size
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    template 'getsize.py'
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    ${task.process}:
+        python: \$(python3 -c 'import platform; print(platform.python_version())')
+        anndata: \$(python3 -c 'import anndata as ad; print(ad.__version__)')
+    END_VERSIONS
+    """
+}

modules/nf-core/anndata/getsize/meta.yml

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+name: "anndata_getsize"
+description: Get the size (n_cells or n_genes) of an anndata object stored as a h5ad file
+keywords:
+  - anndata
+  - single-cell
+  - scanpy
+tools:
+  - "anndata":
+      description: "An annotated data matrix."
+      homepage: "http://anndata.rtfd.io"
+      documentation: "http://anndata.rtfd.io"
+      tool_dev_url: "https://github.com/theislab/anndata"
+      doi: "10.21105/joss.04371"
+      licence: ["BSD-3-clause"]
+      identifier: biotools:anndata
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+    - h5ad:
+        type: file
+        description: H5AD file of anndata object
+        pattern: "*.h5ad"
+
+  - - size_type:
+        type: string
+        description: either 'cells', 'genes', 'obs', or 'var'
+
+output:
+  - size:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.txt":
+          type: file
+          description: text file containing the requested size
+          pattern: "*.txt"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@LeonHafner"
+maintainers:
+  - "@LeonHafner"

modules/nf-core/anndata/getsize/templates/getsize.py

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+#!/usr/bin/env python3
+
+import platform
+
+import anndata as ad
+
+
+def format_yaml_like(data: dict, indent: int = 0) -> str:
+    """Formats a dictionary to a YAML-like string.
+
+    Args:
+        data (dict): The dictionary to format.
+        indent (int): The current indentation level.
+
+    Returns:
+        str: A string formatted as YAML.
+    """
+    yaml_str = ""
+    for key, value in data.items():
+        spaces = "    " * indent
+        if isinstance(value, dict):
+            yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}"
+        else:
+            yaml_str += f"{spaces}{key}: {value}\\n"
+    return yaml_str
+
+
+adata = ad.read_h5ad("${h5ad}", backed="r")
+
+size_functions = {
+    "cells": lambda: adata.n_obs,
+    "genes": lambda: adata.n_vars,
+    "obs": lambda: adata.n_obs,
+    "var": lambda: adata.n_vars,
+}
+
+size_type = "${size_type}".lower()
+if size_type not in size_functions:
+    raise ValueError(f'Size type must be one of {', '.join(size_functions.keys())}.')
+
+size = size_functions[size_type]()
+
+with open("${prefix}.txt", "w") as f:
+    f.write(str(size))
+
+
+# Versions
+versions = {"${task.process}": {"python": platform.python_version(), "anndata": ad.__version__}}
+
+with open("versions.yml", "w") as f:
+    f.write(format_yaml_like(versions))

modules/nf-core/anndata/getsize/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process ANNDATA_GETSIZE"
+    script "../main.nf"
+    process "ANNDATA_GETSIZE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "anndata"
+    tag "anndata/getsize"
+
+    test("scdownstream - h5ad - cells") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_custom_emptydrops_filter_matrix_5k.h5ad', checkIfExists: true),
+                ]
+                input[1] = 'cells'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("scdownstream - h5ad - genes") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_custom_emptydrops_filter_matrix_5k.h5ad', checkIfExists: true),
+                ]
+                input[1] = 'genes'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("scdownstream - h5ad - cells - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_custom_emptydrops_filter_matrix_5k.h5ad', checkIfExists: true),
+                ]
+                input[1] = 'cells'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("scdownstream - h5ad - genes - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430799_custom_emptydrops_filter_matrix_5k.h5ad', checkIfExists: true),
+                ]
+                input[1] = 'genes'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}