Add Freemuxlet to modules (nf-core#5520)

* add freemuxlet * add snapshot * pass container test * remove trailing whitespace * add optional output files creation * remove ldist * fix test * add snapshot --------- Co-authored-by: Xichen Wu <[email protected]> Co-authored-by: wxicu <[email protected]>
adamrtalbot · Apr 30, 2024 · 1f8a032 · 1f8a032
1 parent 891aae4
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diff --git a/modules/nf-core/popscle/freemuxlet/environment.yml b/modules/nf-core/popscle/freemuxlet/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "popscle_freemuxlet"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::popscle=0.1"
diff --git a/modules/nf-core/popscle/freemuxlet/main.nf b/modules/nf-core/popscle/freemuxlet/main.nf
@@ -0,0 +1,61 @@
+process POPSCLE_FREEMUXLET {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/popscle:0.1beta--h2c78cec_0' :
+        'biocontainers/popscle:0.1beta--h2c78cec_0' }"
+
+    input:
+    tuple val(meta), path(plp), val(n_sample)
+
+    output:
+    tuple val(meta), path('*.clust1.samples.gz')  , emit: result
+    tuple val(meta), path('*.clust1.vcf.gz')      , emit: vcf
+    tuple val(meta), path('*.lmix')               , emit: lmix
+    tuple val(meta), path('*.clust0.samples.gz')  , emit: singlet_result   , optional: true
+    tuple val(meta), path('*.clust0.vcf.gz')      , emit: singlet_vcf      , optional: true
+    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 VERSION = '0.1' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    """
+    popscle freemuxlet \\
+        --plp ${plp}/$prefix \\
+        --out $prefix \\
+        --nsample $n_sample \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        popscle: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.1' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+
+    """
+    touch ${prefix}.clust1.samples.gz
+    touch ${prefix}.clust1.vcf.gz
+    touch ${prefix}.lmix
+
+    if [[ "$args" == *"--aux-files"* ]]; then
+        touch ${prefix}.clust0.samples.gz
+        touch ${prefix}.clust0.vcf.gz
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        popscle: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/popscle/freemuxlet/meta.yml b/modules/nf-core/popscle/freemuxlet/meta.yml
@@ -0,0 +1,73 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "popscle_freemuxlet"
+description: Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.
+keywords:
+  - popscle
+  - demultiplexing
+  - genotype-based deconvoltion
+  - single cell
+tools:
+  - "popscle":
+      description: "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools"
+      homepage: "https://github.com/statgen/popscle"
+      documentation: "https://github.com/statgen/popscle"
+      tool_dev_url: "https://github.com/statgen/popscle"
+      doi: "10.1038/nbt.4042"
+      licence: ["Apache-2.0"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1']`
+
+  - plp:
+      type: directory
+      description: Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup.
+  - n_sample:
+      type: integer
+      description: Number of samples multiplexed together.
+
+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"
+
+  - result:
+      type: file
+      description: Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.
+      pattern: "*.clust1.samples.gz"
+
+  - vcf:
+      type: file
+      description: Output vcf file for each sample inferred and clustered from freemuxlet.
+      pattern: "*.clust1.vcf.gz"
+
+  - lmix:
+      type: file
+      description: Output file contains basic statistics for each barcode.
+      pattern: "*.lmix"
+
+  - singlet_result:
+      type: file
+      description: Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.
+      pattern: "*.clust0.samples.gz"
+
+  - singlet_vcf:
+      type: file
+      description: Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.
+      pattern: "*.clust0.vcf.gz"
+
+authors:
+  - "@wxicu"
+maintainers:
+  - "@wxicu"
diff --git a/modules/nf-core/popscle/freemuxlet/tests/main.nf.test b/modules/nf-core/popscle/freemuxlet/tests/main.nf.test
@@ -0,0 +1,183 @@
+nextflow_process {
+
+    name "Test Process POPSCLE_FREEMUXLET"
+    script "../main.nf"
+    process "POPSCLE_FREEMUXLET"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "popscle"
+    tag "popscle/dscpileup"
+    tag "popscle/freemuxlet"
+
+    test("demultiplexing") {
+        setup { 
+            run("POPSCLE_DSCPILEUP") {
+                script "../../dscpileup/main.nf"
+                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),
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ 
+                            plp -> [[ id: 'sample1'], 
+                                    plp[0].getParent(),
+                                    2 ]}
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert path(process.out.result.get(0).get(1)).exists() },
+                { assert path(process.out.vcf.get(0).get(1)).exists() },
+                { assert path(process.out.lmix.get(0).get(1)).exists() }
+            )
+        }
+
+    }
+
+    test("demultiplexing - auxilary - files") {
+        config "./nextflow.config"
+        setup { 
+            run("POPSCLE_DSCPILEUP") {
+                script "../../dscpileup/main.nf"
+                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),
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ 
+                            plp -> [[ id: 'sample1'], 
+                                    plp[0].getParent(),
+                                    2 ]}
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions-aux-files") },
+                { assert path(process.out.result.get(0).get(1)).exists() },
+                { assert path(process.out.vcf.get(0).get(1)).exists() },
+                { assert path(process.out.lmix.get(0).get(1)).exists() },
+                { assert path(process.out.singlet_result.get(0).get(1)).exists() },
+                { assert path(process.out.singlet_vcf.get(0).get(1)).exists() }
+            )
+        }
+
+    }
+
+    test("demultiplexing - stub") {
+
+        options "-stub"
+
+        setup { 
+            run("POPSCLE_DSCPILEUP") {
+                script "../../dscpileup/main.nf"
+                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),
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ 
+                            plp -> [[ id: 'sample1'], 
+                                    plp[0].toString() - '.plp.gz',
+                                    2 ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions-stub") },
+                { assert path(process.out.result.get(0).get(1)).exists() },
+                { assert path(process.out.vcf.get(0).get(1)).exists() },
+                { assert path(process.out.lmix.get(0).get(1)).exists() }
+            )
+        }
+
+    }
+
+    test("demultiplexing - auxilary - files - stub") {
+
+        options "-stub"
+        config "./nextflow.config"
+
+        setup { 
+            run("POPSCLE_DSCPILEUP") {
+                script "../../dscpileup/main.nf"
+                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),
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = POPSCLE_DSCPILEUP.out.plp.collect{ meta, plp -> plp }.map{ 
+                            plp -> [[ id: 'sample1'], 
+                                    plp[0].toString() - '.plp.gz',
+                                    2 ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions-aux-files-stub") },
+                { assert path(process.out.result.get(0).get(1)).exists() },
+                { assert path(process.out.vcf.get(0).get(1)).exists() },
+                { assert path(process.out.lmix.get(0).get(1)).exists() },
+                { assert path(process.out.singlet_result.get(0).get(1)).exists() },
+                { assert path(process.out.singlet_vcf.get(0).get(1)).exists() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/popscle/freemuxlet/tests/main.nf.test.snap b/modules/nf-core/popscle/freemuxlet/tests/main.nf.test.snap
@@ -0,0 +1,50 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,8d90ac14cd657f4c831007418a55910d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-25T12:49:23.684387488"
+    },
+    "versions-aux-files": {
+        "content": [
+            [
+                "versions.yml:md5,8d90ac14cd657f4c831007418a55910d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-25T12:49:35.355844696"
+    },
+    "versions-aux-files-stub": {
+        "content": [
+            [
+                "versions.yml:md5,8d90ac14cd657f4c831007418a55910d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-25T12:49:56.179166814"
+    },
+    "versions-stub": {
+        "content": [
+            [
+                "versions.yml:md5,8d90ac14cd657f4c831007418a55910d"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-25T12:49:45.801327201"
+    }
+}
diff --git a/modules/nf-core/popscle/freemuxlet/tests/nextflow.config b/modules/nf-core/popscle/freemuxlet/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+	withName: POPSCLE_FREEMUXLET {
+    		ext.args = '--aux-files'
+	}
+}
diff --git a/modules/nf-core/popscle/freemuxlet/tests/tags.yml b/modules/nf-core/popscle/freemuxlet/tests/tags.yml
@@ -0,0 +1,2 @@
+popscle/freemuxlet:
+  - "modules/nf-core/popscle/freemuxlet/**"