Add Cellsnp to modules

modules/nf-core/cellsnp/modea/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "cellsnp_modea"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::cellsnp-lite=1.2.3"

modules/nf-core/cellsnp/modea/main.nf

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+process CELLSNP_MODEA {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cellsnp-lite:1.2.3--h6141fd1_2' :
+        'biocontainers/cellsnp-lite:1.2.3--h6141fd1_2' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(region_vcf), path(barcode)
+
+    output:
+    tuple val(meta), path('*.base.vcf.gz') , emit: base
+    tuple val(meta), path('*.cells.vcf.gz'), emit: cell          , optional: true
+    tuple val(meta), path('*.samples.tsv') , emit: sample
+    tuple val(meta), path('*.tag.AD.mtx')  , emit: allele_depth
+    tuple val(meta), path('*.tag.DP.mtx')  , emit: depth_coverage
+    tuple val(meta), path('*.tag.OTH.mtx') , emit: depth_other
+    path 'versions.yml'                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args         = task.ext.args   ?: ''
+    def prefix       = task.ext.prefix ?: "${meta.id}"
+    def region_file  = region_vcf      ? "-R $region_vcf"  : ''
+    """
+    cellsnp-lite -s $bam \\
+        -b $barcode \\
+        $region_file \\
+        -O . \\
+        --gzip \\
+        --nproc $task.cpus \\
+        $args
+
+    mv cellSNP.base.vcf.gz ${prefix}.base.vcf.gz
+    if [[ "$args" == *"--genotype"* ]]; then
+        mv cellSNP.cells.vcf.gz ${prefix}.cells.vcf.gz
+    fi
+    mv cellSNP.tag.AD.mtx ${prefix}.tag.AD.mtx
+    mv cellSNP.tag.DP.mtx ${prefix}.tag.DP.mtx
+    mv cellSNP.tag.OTH.mtx ${prefix}.tag.OTH.mtx
+    mv cellSNP.samples.tsv ${prefix}.samples.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cellsnp: \$(cellsnp-lite --v | awk '{print \$2}')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir $prefix
+    touch ${prefix}.base.vcf.gz
+    touch ${prefix}.samples.tsv
+    touch ${prefix}.tag.AD.mtx
+    touch ${prefix}.tag.DP.mtx
+    touch ${prefix}.tag.OTH.mtx
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cellsnp: \$(cellsnp-lite --v | awk '{print \$2}')
+    END_VERSIONS
+    """
+}

modules/nf-core/cellsnp/modea/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "cellsnp_modea"
+description: Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.
+keywords:
+  - genotyping
+  - single cell
+  - SNP
+  - droplet based single cells
+tools:
+  - "cellsnp":
+      description: "Efficient genotyping bi-allelic SNPs on single cells"
+      homepage: "https://github.com/single-cell-genetics/cellsnp-lite"
+      documentation: "https://cellsnp-lite.readthedocs.io"
+      tool_dev_url: "https://github.com/single-cell-genetics/cellsnp-lite"
+      doi: "10.1093/bioinformatics/btab358"
+      licence: ["Apache-2.0"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - bam:
+      type: file
+      description: A single BAM/SAM/CRAM file, e.g., from CellRanger.
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: The index of the BAM/CRAM file.
+      pattern: "*.{bai,crai}"
+  - region_vcf:
+      type: file
+      description: A optional vcf file listing all candidate SNPs for genotyping.
+      pattern: "*.{vcf, vcf.gz}"
+  - barcode:
+      type: file
+      description: A plain file listing all effective cell barcodes.
+      pattern: "*.tsv"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - base:
+      type: file
+      description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation (without GT).
+      pattern: "*.base.vcf.gz"
+  - cell:
+      type: file
+      description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation & genotype (GT) information for each cell or sample.
+      pattern: "*.cells.vcf.gz"
+  - sample:
+      type: file
+      description: A TSV file listing cell barcodes or sample IDs.
+      pattern: "*.tsv"
+  - allele_depth:
+      type: file
+      description: A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.
+      pattern: "*.tag.AD.mtx"
+  - depth_coverage:
+      type: file
+      description: A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).
+      pattern: "*.tag.DP.mtx"
+  - depth_other:
+      type: file
+      description: A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.
+      pattern: "*.tag.OTH.mtx"
+
+authors:
+  - "@wxicu"
+maintainers:
+  - "@wxicu"

modules/nf-core/cellsnp/modea/tests/main.nf.test

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+// nf-core modules test cellsnp/modea
+nextflow_process {
+
+    name "Test Process CELLSNP_MODEA"
+    script "../main.nf"
+    process "CELLSNP_MODEA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cellsnp"
+    tag "cellsnp/modea"
+    tag "samtools/index"
+
+    test("genotyping") {
+        setup { 
+            run("SAMTOOLS_INDEX") {
+                script "../../../samtools/index/main.nf"
+                process {
+                    """
+                    input[0] = [
+                    [ id:'sample1' ],
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/chr21.bam', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """ 
+
+                input[0] = [[ id: 'sample1'], 
+                            file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/chr21.bam', checkIfExists: true),
+                            SAMTOOLS_INDEX.out.bai.map{it[1]},
+                            file(params.modules_testdata_base_path + /genomics/homo_sapiens/demultiplexing/donor_genotype_chr21.vcf', checkIfExists: true),
+                            file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/barcodes.tsv', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+	            { assert path(process.out.base.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.sample,
+                    process.out.allele_depth,
+                    process.out.depth_coverage,
+                    process.out.depth_other).match()
+                }    
+	        )
+        }
+
+    }
+
+    test("genotyping - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/chr21.bam', checkIfExists: true),
+                    [],
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/donor_genotype_chr21.vcf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/barcodes.tsv', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(
+                    process.out.sample,
+                    process.out.allele_depth,
+                    process.out.depth_coverage,
+                    process.out.depth_other).match("stub")
+            },
+	        { assert path(process.out.base.get(0).get(1)).exists() } )
+
+
+        }
+    }
+
+}

modules/nf-core/cellsnp/modea/tests/main.nf.test.snap

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+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,965121af3dc48657c2128c404589fa6b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-05T18:34:17.845506428"
+    },
+    "genotyping": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.samples.tsv:md5,9e488782c1bcd63c37ee3d1c4c0a9217"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.tag.AD.mtx:md5,dbe2d13dca2717749554d1f2a8b85650"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.tag.DP.mtx:md5,29fbb6241c6c7b0a0fa31021e622c415"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.tag.OTH.mtx:md5,1e3429950c59edec58a80a9b4ecda552"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-05T18:34:17.88339067"
+    },
+    "stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.tag.AD.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.tag.DP.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "sample1.tag.OTH.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-05T18:34:29.159643061"
+    }
+}

modules/nf-core/cellsnp/modea/tests/tags.yml

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+cellsnp/modea:
+  - "modules/nf-core/cellsnp/modea/**"