new module - bamstats generalstats

modules/nf-core/bamstats/generalstats/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "bamstats_generalstats"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::bamstats=0.3.5"

modules/nf-core/bamstats/generalstats/main.nf

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+process BAMSTATS_GENERALSTATS {
+    tag "$meta.id"
+    label 'process_single'
+    conda "bioconda::bamstats=0.3.5"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bamstats:0.3.5--he881be0_0':
+        'biocontainers/bamstats:0.3.5--he881be0_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    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}"
+    // Several ARGS are available.
+    //  -a is a helpfu; one where you can add a BED file
+    //  -u, --uniq outputs genomic coverage statistics for uniqely mapped reads
+    """
+    bamstats \\
+        -i $bam \\
+        $args \\
+        -c $task.cpus \\
+        -o ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamstats: \$(echo \$(bamstats --version 2>&1) | sed 's/^.*bamstats == version://; s/Using.*\$//' | sed 's/built.*//' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamstats: \$(echo \$(bamstats --version 2>&1) | sed 's/^.*bamstats == version://; s/Using.*\$//' | sed 's/built.*//' )
+    END_VERSIONS
+    """
+}
+

modules/nf-core/bamstats/generalstats/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "bamstats_generalstats"
+description: write your description here
+keywords:
+  - bam
+  - statistics
+  - genomics
+tools:
+  - "bamstats":
+      description: "A command line tool to compute mapping statistics from a BAM file"
+      homepage: "https://github.com/guigolab/bamstats/"
+      documentation: "https://github.com/guigolab/bamstats/"
+      tool_dev_url: "https://github.com/guigolab"
+      licence: ["BSD-3-clause"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: json containing bam statistics
+      pattern: "*.json"
+
+authors:
+  - "@johnoooh"

modules/nf-core/bamstats/generalstats/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process BAMSTATS_GENERALSTATS"
+    script "../main.nf"
+    process "BAMSTATS_GENERALSTATS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bamstats"
+    tag "bamstats/generalstats"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json.get(0)[1]).exists() },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.json.get(0)[1]).exists() },
+                { assert snapshot(process.out.versions).match("versions_stub") }
+            )
+        }
+
+    }
+
+}

modules/nf-core/bamstats/generalstats/tests/tags.yml

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+bamstats/generalstats:
+  - "modules/nf-core/bamstats/generalstats/**"