add fgumi sort/zipper modules

modules/nf-core/fgumi/sort/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fgumi=0.1.2
+  - conda-forge::r-base=4.5.3
+  - conda-forge::r-ggplot2=4.0.2
+  - conda-forge::r-scales=1.4.0

modules/nf-core/fgumi/sort/main.nf

@@ -0,0 +1,44 @@
+process FGUMI_SORT {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/954170443a820787c9e02ef2135ebb8ec29c6b03633b0d61b5fafa98c59a1cce/data'
+        : 'community.wave.seqera.io/library/fgumi_r-base_r-ggplot2_r-scales:09c99070b82c1c28'}"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.bam.bai"), emit: bai, optional: true
+    tuple val("${task.process}"), val('fgumi'), eval("fgumi --version | sed -n 's/^fgumi //p'"), topic: versions, emit: versions_fgumi
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    fgumi sort \\
+        ${args} \\
+        --threads ${task.cpus} \\
+        --tmp-dir \$PWD \\
+        --input ${bam} \\
+        --output ${prefix}.bam
+
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo ${args}
+
+    touch ${prefix}.bam
+    """
+}

modules/nf-core/fgumi/sort/meta.yml

@@ -0,0 +1,79 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fgumi_sort"
+description: Sort a BAM file using high-performance external merge-sort
+keywords:
+  - sort
+  - bam
+  - sam
+tools:
+  - "fgumi":
+      description: "High-performance tools for UMI-tagged sequencing data."
+      homepage: "https://github.com/fulcrumgenomics/fgumi/blob/v0.1.2/README.md"
+      documentation: "https://github.com/fulcrumgenomics/fgumi/blob/v0.1.2/README.md"
+      tool_dev_url: "https://github.com/fulcrumgenomics/fgumi"
+      licence: ["MIT"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bam:
+        type: file
+        description: Unsorted BAM file
+        pattern: "*.{bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572" # BAM
+
+output:
+  bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.bam":
+          type: file
+          description: Sorted BAM file
+          pattern: "*.{bam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+  bai:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.bam.bai":
+          type: file
+          description: BAM index file
+          pattern: "*.bam.bai"
+          ontologies:
+            - edam: "http://edamontology.org/format_2573" # BAM index
+  versions_fgumi:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "fgumi":
+          type: string
+          description: The name of the tool
+      - "fgumi --version | sed -n 's/^fgumi //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fgumi:
+          type: string
+          description: The name of the tool
+      - fgumi --version | sed -n 's/^fgumi //p':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@matthdsm"
+maintainers:
+  - "@matthdsm"

modules/nf-core/fgumi/sort/tests/main.nf.test

@@ -0,0 +1,97 @@
+nextflow_process {
+
+    name "Test Process FGUMI_SORT"
+    script "../main.nf"
+    process "FGUMI_SORT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fgumi"
+    tag "fgumi/sort"
+
+    test("bam - coordinate sort - index") {
+
+        when {
+            params {
+                fgumi_args = '--order coordinate --write-index'
+            }
+            process {
+                """
+                input[0] = [
+                            [ id:'test', single_end:false ],
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+    test("bam - queryname sort - no index") {
+
+        when {
+            params {
+                fgumi_args = '--order queryname'
+            }
+            process {
+                """
+                input[0] = [
+                            [ id:'test', single_end:false ],
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+    test("bam - coordinate sort - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                fgumi_args = '--order coordinate --write-index'
+            }
+            process {
+                """
+                input[0] = [
+                            [ id:'test', single_end:false ],
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/fgumi/sort/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: FGUMI_SORT {
+        ext.args = params.fgumi_args
+    }
+}

modules/nf-core/fgumi/zipper/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::fgumi=0.1.2
+  - conda-forge::r-base=4.5.3
+  - conda-forge::r-ggplot2=4.0.2
+  - conda-forge::r-scales=1.4.0

modules/nf-core/fgumi/zipper/main.nf

@@ -0,0 +1,43 @@
+process FGUMI_ZIPPER {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/954170443a820787c9e02ef2135ebb8ec29c6b03633b0d61b5fafa98c59a1cce/data'
+        : 'community.wave.seqera.io/library/fgumi_r-base_r-ggplot2_r-scales:09c99070b82c1c28'}"
+
+    input:
+    tuple val(meta), path(mapped, stageAs: "mapped/*"), path(unmapped, stageAs: "unmapped/*")
+    tuple val(meta2), path(fasta), path(fasta_index), path(fasta_dict)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val("${task.process}"), val('fgumi'), eval("fgumi --version | sed -n 's/^fgumi //p'"), topic: versions, emit: versions_fgumi
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    fgumi zipper \\
+        ${args} \\
+        --input ${mapped} \\
+        --unmapped ${unmapped} \\
+        --reference ${fasta} \\
+        --threads ${task.cpus} \\
+        --output ${prefix}.bam
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch ${prefix}.bam
+    """
+}

modules/nf-core/fgumi/zipper/meta.yml

@@ -0,0 +1,98 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fgumi_zipper"
+description: Merge unmapped and mapped BAM files, transferring tags and metadata.
+keywords:
+  - fgbio
+  - umi
+  - unmapped
+  - ubam
+  - zipperbams
+tools:
+  - "fgumi":
+      description: "High-performance tools for UMI-tagged sequencing data."
+      homepage: "https://github.com/fulcrumgenomics/fgumi/blob/v0.1.2/README.md"
+      documentation: "https://github.com/fulcrumgenomics/fgumi/blob/v0.1.2/README.md"
+      tool_dev_url: "https://github.com/fulcrumgenomics/fgumi"
+      licence: ["MIT"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - mapped:
+        type: file
+        description: mapped BAM/SAM file
+        pattern: "*.{bam, sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572" # BAM
+          - edam: "http://edamontology.org/format_3462" # SAM
+    - unmapped:
+        type: file
+        description: unmapped BAM file
+        pattern: "*.bam"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572" # BAM
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'GRCh38' ]`
+    - fasta:
+        type: file
+        description: fasta file containing genomic sequence information
+        pattern: "*.{fasta,fna,fa}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929" # FASTA
+    - fasta_index:
+        type: file
+        description: fasta index file
+        pattern: "*.fai"
+        ontologies:
+          - edam: "http://edamontology.org/format_2573" # BAM index
+    - fasta_dict:
+        type: file
+        description: dict file containing a sequence dictionary for the fasta file
+        pattern: "*.dict"
+        ontologies: []
+
+output:
+  bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.bam":
+          type: file
+          description: Merged BAM file
+          pattern: "*.{bam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+  versions_fgumi:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "fgumi":
+          type: string
+          description: The name of the tool
+      - "fgumi --version | sed -n 's/^fgumi //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fgumi:
+          type: string
+          description: The name of the tool
+      - fgumi --version | sed -n 's/^fgumi //p':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@matthdsm"
+maintainers:
+  - "@matthdsm"