Add scds module

modules/nf-core/scds/environment.yml

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+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-scds=1.18.0
+  - conda-forge::r-seurat=5.1.0
+  - conda-forge::r-xgboost=1.7.6

modules/nf-core/scds/main.nf

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+process SCDS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bioconductor-scds:1.18.0--r43hdfd78af_0':
+        'biocontainers/bioconductor-scds:1.18.0--r43hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(rds)
+
+    output:
+    tuple val(meta), path("*.rds"), emit: rds
+    tuple val(meta), path("*.csv"), emit: predictions
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    template 'scds.R'
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.rds
+    touch ${prefix}.csv
+    touch versions.yml
+    """
+}

modules/nf-core/scds/meta.yml

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+---
+name: scds
+description: Module to use scds for doublet scoring
+keywords:
+  - doublet
+  - single-cell
+  - transcriptomics
+tools:
+  - scds:
+      description: scds is an in-silico doublet annotation tool for single cell RNA sequencing data
+      homepage: https://www.bioconductor.org/packages/release/bioc/html/scds.html
+      documentation: https://www.bioconductor.org/packages/release/bioc/vignettes/scds/inst/doc/scds.html
+      tool_dev_url: https://github.com/kostkalab/scds
+      doi: 10.1093/bioinformatics/btz698
+      licence: ["MIT"]
+      identifier: biotools:scds
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - rds:
+        type: file
+        description: RDS file containing filtered data (without empty droplets) in SingleCellExperiment format
+        pattern: "*.rds"
+
+output:
+  - rds:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.rds":
+          type: file
+          description: RDS file containing doublet scores in SingleCellExperiment format
+          pattern: "*.rds"
+  - predictions:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.csv":
+          type: file
+          description: CSV file containing doublet scores
+          pattern: "*.csv"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software version
+          pattern: "versions.yml"
+
+authors:
+  - "@cakirb"
+maintainers:
+  - "@cakirb"

modules/nf-core/scds/templates/scds.R

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+#!/usr/bin/env Rscript
+
+library(scds)
+library(SingleCellExperiment)
+
+sce <- readRDS("${rds}")
+
+sce <- Seurat::as.SingleCellExperiment(sce)
+
+## Annotate doublet using binary classification based doublet scoring:
+sce <- bcds(sce, retRes = TRUE, estNdbl=TRUE)
+
+## Annotate doublet using co-expression based doublet scoring:
+try({
+    sce <- cxds(sce, retRes = TRUE, estNdbl=TRUE)
+})
+
+### If cxds worked, run hybrid, otherwise use bcds annotations
+if ("cxds_score" %in% colnames(colData(sce))) {
+    ## Combine both annotations into a hybrid annotation
+    sce <- cxds_bcds_hybrid(sce, estNdbl=TRUE)
+
+    predictions <- colData(sce)[, 'hybrid_call', drop=FALSE]
+} else {
+    predictions <- colData(sce)[, 'bcds_call', drop=FALSE]
+}
+
+saveRDS(sce, "${prefix}.rds")
+
+colnames(predictions) <- "${prefix}"
+write.csv(predictions, "${prefix}.csv")
+
+################################################
+################################################
+## VERSIONS FILE                              ##
+################################################
+################################################
+
+r.version <- strsplit(version[['version.string']], ' ')[[1]][3]
+scds.version <- as.character(packageVersion('scds'))
+
+writeLines(
+    c(
+        '"${task.process}":',
+        paste('    R:', r.version),
+        paste('    scds:', scds.version)
+    ),
+'versions.yml')
+
+################################################
+################################################
+################################################
+################################################

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

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+nextflow_process {
+    name 'Test Process SCDS'
+    script '../main.nf'
+    process 'SCDS'
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "scds"
+
+    test("test_scds") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix.rds", checkIfExists: true)                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(process.out.rds).match("res_scds_rds")},
+                {assert snapshot(process.out.csv).match("res_scds_csv")},
+                {assert snapshot(process.out.versions).match("res_scds_versions")}
+            )
+        }
+    }
+
+    test("test_scds - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/scdownstream/samples/SAMN14430801_custom_emptydrops_filter_matrix.rds", checkIfExists: true)                ]
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(process.out.rds).match("res_scds_rds_stub")},
+                {assert snapshot(process.out.csv).match("res_scds_csv_stub")},
+                {assert snapshot(process.out.versions).match("res_scds_versions_stub")}
+            )
+        }
+    }
+}

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

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+{
+    "res_scds_csv": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T11:50:55.821158"
+    },
+    "res_scds_versions": {
+        "content": [
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T11:50:55.827718"
+    },
+    "res_scds_rds": {
+        "content": [
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T11:50:55.808717"
+    }
+}