Add pbcpgtools/alignedbamtocpgscores module

modules/nf-core/pbcpgtools/alignedbamtocpgscores/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::pb-cpg-tools=3.0.0"

modules/nf-core/pbcpgtools/alignedbamtocpgscores/main.nf

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+process PBCPGTOOLS_ALIGNEDBAMTOCPGSCORES {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pb-cpg-tools:3.0.0--h9ee0642_0':
+        'biocontainers/pb-cpg-tools:3.0.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+
+    output:
+    tuple val(meta), path("*.combined.bed.gz")    , emit: combined_bed
+    tuple val(meta), path("*.combined.bed.gz.tbi"), emit: combined_bed_index
+    tuple val(meta), path("*.combined.bw")        , emit: combined_bigwig
+    tuple val(meta), path("*.hap1.bed.gz")        , emit: hap1_bed          , optional: true
+    tuple val(meta), path("*.hap1.bed.gz.tbi")    , emit: hap1_bed_index    , optional: true
+    tuple val(meta), path("*.hap1.bw")            , emit: hap1_bigwig       , optional: true
+    tuple val(meta), path("*.hap2.bed.gz")        , emit: hap2_bed          , optional: true
+    tuple val(meta), path("*.hap2.bed.gz.tbi")    , emit: hap2_bed_index    , optional: true
+    tuple val(meta), path("*.hap2.bw")            , emit: hap2_bigwig       , optional: true
+    path "versions.yml"                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    aligned_bam_to_cpg_scores \\
+        --bam ${bam} \\
+        --output-prefix ${prefix} \\
+        --threads ${task.cpus} \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbcpgtools: \$(aligned_bam_to_cpg_scores --version | sed 's/.* //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.combined.bed.gz
+    touch ${prefix}.combined.bed.gz.tbi
+    touch ${prefix}.combined.bw
+
+    echo "" | gzip > ${prefix}.hap1.bed.gz
+    touch ${prefix}.hap1.bed.gz.tbi
+    touch ${prefix}.hap1.bw
+
+    echo "" | gzip > ${prefix}.hap2.bed.gz
+    touch ${prefix}.hap2.bed.gz.tbi
+    touch ${prefix}.hap2.bw
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pbcpgtools: \$(aligned_bam_to_cpg_scores --version | sed 's/.* //')
+    END_VERSIONS
+    """
+}

modules/nf-core/pbcpgtools/alignedbamtocpgscores/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pbcpgtools_alignedbamtocpgscores"
+description: Converts aligned BAM files into CpG methylation scores
+keywords:
+  - methylation
+  - cpg
+  - pacbio
+tools:
+  - pbcpgtools:
+      description: "Collection of tools for the analysis of CpG data"
+      homepage: "https://github.com/PacificBiosciences/pb-CpG-tools"
+      documentation: "https://github.com/PacificBiosciences/pb-CpG-tools#readme"
+      tool_dev_url: "https://github.com/PacificBiosciences/pb-CpG-tools"
+      licence: ["Pacific Biosciences Software License Agreement"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test' ]`
+    - bam:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.{bam,cram}"
+        ontologies: []
+    - bai:
+        type: file
+        description: Index of BAM/CRAM file
+        pattern: "*.{bai,crai,csi}"
+        ontologies: []
+output:
+  combined_bed:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.combined.bed.gz":
+          type: file
+          description: Zipped BED file with CpG methylation scores for both haplotypes
+          pattern: "*.{combined.bed.gz}"
+          ontologies: []
+  combined_bed_index:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.combined.bed.gz.tbi":
+          type: file
+          description: Index of combined zipped BED file
+          pattern: "*.{combined.bed.gz.tbi}"
+          ontologies: []
+  combined_bigwig:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.combined.bw":
+          type: file
+          description: Bigwig file for visualization in IGV
+          pattern: "*.{combined.bw}"
+          ontologies: []
+  hap1_bed:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.hap1.bed.gz":
+          type: file
+          description: Zipped BED file with CpG methylation scores for haplotype 1
+          pattern: "*.{hap1.bed.gz}"
+          ontologies: []
+  hap1_bed_index:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.hap1.bed.gz.tbi":
+          type: file
+          description: Index of hap1 zipped BED file
+          pattern: "*.{hap1.bed.gz.tbi}"
+          ontologies: []
+  hap1_bigwig:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.hap1.bw":
+          type: file
+          description: Bigwig file for visualization in IGV
+          pattern: "*.{hap1.bw}"
+          ontologies: []
+  hap2_bed:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.hap2.bed.gz":
+          type: file
+          description: Zipped BED file with CpG methylation scores for haplotype 2
+          pattern: "*.{hap2.bed.gz}"
+          ontologies: []
+  hap2_bed_index:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.hap2.bed.gz.tbi":
+          type: file
+          description: Index of hap2 zipped BED file
+          pattern: "*.{hap2.bed.gz.tbi}"
+          ontologies: []
+  hap2_bigwig:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*.hap2.bw":
+          type: file
+          description: Bigwig file for visualization in IGV
+          pattern: "*.{hap2.bw}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@inemesb"
+maintainers:
+  - "@inemesb"

modules/nf-core/pbcpgtools/alignedbamtocpgscores/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process PBCPGTOOLS_ALIGNEDBAMTOCPGSCORES"
+    script "../main.nf"
+    process "PBCPGTOOLS_ALIGNEDBAMTOCPGSCORES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pbcpgtools"
+    tag "pbcpgtools/alignedbamtocpgscores"
+
+    test("pacbio - bam - notphased") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA037562_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA037562_downsampled.pbmm2.repeats.bam.bai', checkIfExists: true)
+
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("pacbio - bam - phased") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA037562_downsampled.pbmm2.repeats.phased.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA037562_downsampled.pbmm2.repeats.phased.bam.bai', checkIfExists: true)
+
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("pacbio - bam - phased - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA037562_downsampled.pbmm2.repeats.phased.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA037562_downsampled.pbmm2.repeats.phased.bam.bai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}