Adding module bamtools stats (#2104)

* added bamtools stats module and tested

* added bamtools stats module and tested

* fixing prettier complaints

* changed process tag to single

modules/bamtools/stats/main.nf

@@ -0,0 +1,35 @@
+process BAMTOOLS_STATS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
+        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.stats"), emit: stats
+    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}"
+
+    """
+    bamtools \\
+        stats \\
+        -in $bam \\
+        >${prefix}.bam.stats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
+    END_VERSIONS
+    """
+}

modules/bamtools/stats/meta.yml

@@ -0,0 +1,43 @@
+name: "bamtools_stats"
+description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
+keywords:
+  - bamtools
+  - stats
+  - bam
+tools:
+  - bamtools:
+      description: C++ API & command-line toolkit for working with BAM data
+      homepage: http://github.com/pezmaster31/bamtools
+      documentation: https://github.com/pezmaster31/bamtools/wiki
+      tool_dev_url: http://github.com/pezmaster31/bamtools
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+
+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"
+  - stats:
+      type: file
+      description: File containing alignment statistics
+      pattern: "*.stats"
+
+authors:
+  - "@lescai"

tests/config/pytest_modules.yml

@@ -126,6 +126,10 @@ bamtools/split:
   - modules/bamtools/split/**
   - tests/modules/bamtools/split/**
 
+bamtools/stats:
+  - modules/bamtools/stats/**
+  - tests/modules/bamtools/stats/**
+
 bamutil/trimbam:
   - modules/bamutil/trimbam/**
   - tests/modules/bamutil/trimbam/**

tests/modules/bamtools/stats/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMTOOLS_STATS } from '../../../../modules/bamtools/stats/main.nf'
+
+workflow test_bamtools_stats {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_STATS ( input )
+}

tests/modules/bamtools/stats/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/bamtools/stats/test.yml

@@ -0,0 +1,8 @@
+- name: bamtools stats test_bamtools_stats
+  command: nextflow run ./tests/modules/bamtools/stats -entry test_bamtools_stats -c ./tests/config/nextflow.config  -c ./tests/modules/bamtools/stats/nextflow.config
+  tags:
+    - bamtools/stats
+    - bamtools
+  files:
+    - path: output/bamtools/test.bam.stats
+      md5sum: b7c3f01682673a652d664a2889b15b66