Add module fgbio/collectduplexseqmetrics (#5960)

* Initial commit

* Rerun nf-test

* Change assertion for duplex_qc output

* Add ggplot2 to version.yml

* Update snapshot

* Correct conda packages version

modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "fgbio_collectduplexseqmetrics"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::fgbio=2.0.2"
+  - "conda-forge::r-ggplot2=3.4.4"

modules/nf-core/fgbio/collectduplexseqmetrics/main.nf

@@ -0,0 +1,80 @@
+process FGBIO_COLLECTDUPLEXSEQMETRICS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-51891ad0b60843e4aade9cde2eb5d40c5ae92b80:72c944cdea5caff7f03b96034968ce2a4f1737bc-0':
+        'biocontainers/mulled-v2-51891ad0b60843e4aade9cde2eb5d40c5ae92b80:72c944cdea5caff7f03b96034968ce2a4f1737bc-0' }"
+
+    input:
+    tuple val(meta), path(grouped_bam)
+    path interval_list
+
+    output:
+    tuple val(meta), path("**.family_sizes.txt")        , emit: family_sizes
+    tuple val(meta), path("**.duplex_family_sizes.txt") , emit: duplex_family_sizes
+    tuple val(meta), path("**.duplex_yield_metrics.txt"), emit: duplex_yield_metrics
+    tuple val(meta), path("**.umi_counts.txt")          , emit: umi_counts
+    tuple val(meta), path("**.duplex_qc.pdf")           , emit: duplex_qc
+    tuple val(meta), path("**.duplex_umi_counts.txt")   , emit: duplex_umi_counts, optional: true
+    path "versions.yml"                                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals = interval_list ? "--intervals ${bed}" : ""
+    def mem_gb = 8
+
+    if (!task.memory) {
+        log.info '[fgbio CollectDuplexSeqMetrics] Available memory not known - defaulting to 8GB. Specify process memory requirements to change this.'
+    } else if (mem_gb > task.memory.giga) {
+        if (task.memory.giga < 2) {
+            mem_gb = 1
+        } else {
+            mem_gb = task.memory.giga - 1
+        }
+    }
+
+    """
+    fgbio \\
+        -Xmx${mem_gb}g \\
+        --tmp-dir=. \\
+        --async-io=true \\
+        --compression=1 \\
+        CollectDuplexSeqMetrics \\
+        --input $grouped_bam \\
+        --output ${prefix} \\
+        $intervals \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+        ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def touch_duplex_umi = args.contains("--duplex-umi-counts") || args.contains("-u") ? "touch ${prefix}.duplex_umi_counts.txt" : ""
+
+    """
+    touch ${prefix}.family_sizes.txt
+    touch ${prefix}.duplex_family_sizes.txt
+    touch ${prefix}.duplex_yield_metrics.txt
+    touch ${prefix}.umi_counts.txt
+    touch ${prefix}.duplex_qc.pdf
+    $touch_duplex_umi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+        ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
+    END_VERSIONS
+    """
+}

modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml

@@ -0,0 +1,78 @@
+---
+name: "fgbio_collectduplexseqmetrics"
+description: Collects a suite of metrics to QC duplex sequencing data.
+keywords:
+  - UMIs
+  - QC
+  - bam
+  - duplex
+tools:
+  - "fgbio":
+      description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs"
+      homepage: "http://fulcrumgenomics.github.io/fgbio/"
+      documentation: "http://fulcrumgenomics.github.io/fgbio/"
+      tool_dev_url: "https://github.com/fulcrumgenomics/fgbio"
+      licence: ["MIT"]
+  - "r-ggplot2":
+      description: "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics. "
+      homepage: "https://ggplot2.tidyverse.org/"
+      documentation: "https://ggplot2.tidyverse.org/"
+      tool_dev_url: "https://github.com/tidyverse/ggplot2"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+
+  - grouped_bam:
+      type: file
+      description: It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order.
+      pattern: "*.bam"
+
+  - interval_list:
+      type: file
+      description: Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here  https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html
+      pattern: "*.{tsv|txt|interval_list}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - family_sizes:
+      type: file
+      description: Metrics on the frequency of different types of families of different sizes
+      pattern: "*.txt"
+  - duplex_family_sizes:
+      type: file
+      description: Metrics on the frequency of duplex tag families by the number of observations from each strand
+      pattern: "*.txt"
+  - duplex_yield_metrics:
+      type: file
+      description: Summary QC metrics produced using 5%, 10%, 15%...100% of the data
+      pattern: "*.txt"
+  - umi_counts:
+      type: file
+      description: Metrics on the frequency of observations of UMIs within reads and tag families
+      pattern: "*.txt"
+  - duplex_qc:
+      type: file
+      description: A series of plots generated from the preceding metrics files for visualization
+      pattern: "*.pdf"
+  - duplex_umi_counts:
+      type: file
+      description: Metrics on the frequency of observations of duplex UMIs within reads and tag families.
+      pattern: "*.txt"
+
+authors:
+  - "@georgiakes"
+maintainers:
+  - "@georgiakes"

modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test

@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process FGBIO_COLLECTDUPLEXSEQMETRICS"
+    script "../main.nf"
+    process "FGBIO_COLLECTDUPLEXSEQMETRICS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fgbio"
+    tag "fgbio/collectduplexseqmetrics"
+
+
+    test("homo_sapiens - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true)
+                ]
+                input[1]=[]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.family_sizes,
+                process.out.duplex_family_sizes,
+                process.out.duplex_yield_metrics,
+                process.out.umi_counts,
+                process.out.duplex_umi_counts,
+                process.out.versions,
+                file(process.out.duplex_qc[0][1]).name)
+                .match() }
+
+            )
+        }
+
+    }
+
+    test("homo_sapiens - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true)
+                ]
+                input[1] = []
+
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.family_sizes,
+                process.out.duplex_family_sizes,
+                process.out.duplex_yield_metrics,
+                process.out.umi_counts,
+                process.out.duplex_umi_counts,
+                process.out.versions,
+                file(process.out.duplex_qc[0][1]).name)
+                .match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap

@@ -0,0 +1,106 @@
+{
+    "homo_sapiens - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_yield_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.umi_counts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+
+            ],
+            [
+                "versions.yml:md5,637a7384cd910f0e0541a631c52b95e1"
+            ],
+            "test.duplex_qc.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T19:26:23.325859809"
+    },
+    "homo_sapiens - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.family_sizes.txt:md5,a49de49bd587440c316fec830f502620"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_family_sizes.txt:md5,129e41170b9f5f2f8edce62a686c8548"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_yield_metrics.txt:md5,237e4e4ee713fdf672b0ee796827fb9d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.umi_counts.txt:md5,9fe38b2a49ca80492b3a1c6a55679155"
+                ]
+            ],
+            [
+
+            ],
+            [
+                "versions.yml:md5,637a7384cd910f0e0541a631c52b95e1"
+            ],
+            "test.duplex_qc.pdf"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-17T19:26:03.1373243"
+    }
+}

modules/nf-core/fgbio/collectduplexseqmetrics/tests/tags.yml

@@ -0,0 +1,2 @@
+fgbio/collectduplexseqmetrics:
+  - "modules/nf-core/fgbio/collectduplexseqmetrics/**"