new module: PERBASE

modules/nf-core/perbase/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::perbase=0.10.2

modules/nf-core/perbase/main.nf

@@ -0,0 +1,52 @@
+process PERBASE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/perbase:0.10.2--h15397dd_0':
+        'biocontainers/perbase:0.10.2--h15397dd_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(index)
+    tuple val(meta2), path(fasta), path(fai)
+
+    output:
+    tuple val(meta), path("*.tsv.gz"), emit: tsv
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = fasta ? "--ref-fasta ${fasta}" : ""
+    """
+    perbase \\
+        base-depth \\
+        $bam \\
+        $args \\
+        $reference \\
+        --threads $task.cpus \\
+        --bgzip \\
+        --output ${prefix}.tsv.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        perbase: \$(perbase --version |& sed '1!d ; s/perbase //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.tsv.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        perbase: \$(perbase --version |& sed '1!d ; s/perbase //')
+    END_VERSIONS
+    """
+}

modules/nf-core/perbase/meta.yml

@@ -0,0 +1,77 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "perbase"
+description: Per-base metrics on BAM/CRAM files.
+keywords:
+  - bam
+  - cram
+  - depth
+tools:
+  - "perbase":
+      description: "Per-base metrics on BAM/CRAM files."
+      homepage: "https://github.com/sstadick/perbase/blob/v0.10.2/README.md"
+      documentation: "https://github.com/sstadick/perbase/blob/v0.10.2/README.md"
+      tool_dev_url: "https://github.com/sstadick/perbase"
+      licence: ["MIT"]
+      identifier: biotools:perbase
+
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM file
+        pattern: "*.{bam,cram}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_3462"
+
+    - index:
+        type: file
+        description: BAI/CRAI file
+        pattern: "*.{bai,crai}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3327"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference fasta (optional)
+        pattern: "*.{fasta,fa}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+    - fai:
+        type: file
+        description: FAI file (optional)
+        pattern: "*.{fai}"
+output:
+  - tsv:
+      #Only when we have meta
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.tsv.gz":
+          type: file
+          description: TSV file
+          pattern: "*.{tsv.gz}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@camlloyd"
+maintainers:
+  - "@camlloyd"

modules/nf-core/perbase/tests/main.nf.test

@@ -0,0 +1,126 @@
+nextflow_process {
+
+    name "Test Process PERBASE"
+    script "../main.nf"
+    process "PERBASE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "perbase"
+
+    test("homo_sapiens - illumina - cram") {
+
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - illumina - cram - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+        test("homo_sapiens - illumina - bam") {
+
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [[],[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - illumina - bam - 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/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [[],[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}