New module: bamtools/convert (#1219)

* 📦 NEW: Add bamtools/convert module

* 👌 IMPROVE: Update output channel name, Add tests for each output format

* 👌 IMPROVE: Add error test

* 🐛 FIX: Remove custom tags

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

modules/bamtools/convert/main.nf

@@ -0,0 +1,38 @@
+process BAMTOOLS_CONVERT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    container "${ 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("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
+    path "versions.yml"                                              , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
+    if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
+    m = args =~ /-format ([a-z]+)/
+    ext = m[0][1]
+
+
+    """
+    bamtools \\
+        convert \\
+        $args \\
+        -in $bam \\
+        -out ${prefix}.${ext}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
+    END_VERSIONS
+    """
+}

modules/bamtools/convert/meta.yml

@@ -0,0 +1,52 @@
+name: bamtools_convert
+description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
+keywords:
+  - bamtools
+  - bamtools/convert
+  - bam
+  - convert
+  - bed
+  - fasta
+  - fastq
+  - json
+  - pileup
+  - sam
+  - yaml
+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"
+  ## TODO nf-core: Delete / customise this example output
+  - out:
+      type: file
+      description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
+      pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"
+
+authors:
+  - "@sguizard"

tests/config/pytest_modules.yml

@@ -46,6 +46,10 @@ bamaligncleaner:
   - modules/bamaligncleaner/**
   - tests/modules/bamaligncleaner/**
 
+bamtools/convert:
+  - modules/bamtools/convert/**
+  - tests/modules/bamtools/convert/**
+
 bamtools/split:
   - modules/bamtools/split/**
   - tests/modules/bamtools/split/**

tests/modules/bamtools/convert/main.nf

@@ -0,0 +1,104 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR }   from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED }         from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA }       from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ }       from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON }        from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP }      from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM }         from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML }        from '../../../../modules/bamtools/convert/main.nf'
+
+workflow test_bamtools_convert_ext_error {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_EXT_ERROR ( input )
+}
+
+workflow test_bamtools_convert_noext_error {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
+}
+
+workflow test_bamtools_convert_bed {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_BED ( input )
+}
+
+workflow test_bamtools_convert_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_FASTA ( input )
+}
+
+workflow test_bamtools_convert_fastq {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_FASTQ ( input )
+}
+
+workflow test_bamtools_convert_json {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_JSON ( input )
+}
+
+workflow test_bamtools_convert_pileup {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_PILEUP ( input )
+}
+
+workflow test_bamtools_convert_sam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_SAM ( input )
+}
+
+workflow test_bamtools_convert_yaml {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_YAML ( input )
+}
+

tests/modules/bamtools/convert/nextflow.config

@@ -0,0 +1,41 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: BAMTOOLS_CONVERT_EXT_ERROR {
+        ext.args = "-format vcf"
+    }
+
+    withName: BAMTOOLS_CONVERT_NOEXT_ERROR {
+        ext.args = ""
+    }
+
+    withName: BAMTOOLS_CONVERT_BED {
+        ext.args = "-format bed"
+    }
+
+    withName: BAMTOOLS_CONVERT_FASTA {
+        ext.args = "-format fasta"
+    }
+
+    withName: BAMTOOLS_CONVERT_FASTQ {
+        ext.args = "-format fastq"
+    }
+
+    withName: BAMTOOLS_CONVERT_JSON {
+        ext.args = "-format json"
+    }
+
+    withName: BAMTOOLS_CONVERT_PILEUP {
+        ext.args = "-format pileup"
+    }
+
+    withName: BAMTOOLS_CONVERT_SAM {
+        ext.args = "-format sam"
+    }
+
+    withName: BAMTOOLS_CONVERT_YAML {
+        ext.args = "-format yaml"
+    }
+
+}

tests/modules/bamtools/convert/test.yml

@@ -0,0 +1,90 @@
+- name: bamtools convert test_bamtools_convert_ext_error
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  exit_code: 1
+
+- name: bamtools convert test_bamtools_convert_noext_error
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  exit_code: 1
+
+- name: bamtools convert test_bamtools_convert_bed
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.bed
+      md5sum: 4e34cc15bf31e700f5f3a9f8fffb6c81
+    - path: output/bamtools/versions.yml
+      md5sum: eb7a144b8a97965d3482f6f96b8a8243
+
+- name: bamtools convert test_bamtools_convert_fasta
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.fasta
+      md5sum: 52aeacf78571862b7e97c7d44ac8f827
+    - path: output/bamtools/versions.yml
+      md5sum: 42d19a2b2b07f05edb82b34369dfd754
+
+- name: bamtools convert test_bamtools_convert_fastq
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.fastq
+      md5sum: e591c48daad2c56638e5d6f21f1f71c5
+    - path: output/bamtools/versions.yml
+      md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e
+
+- name: bamtools convert test_bamtools_convert_json
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.json
+      md5sum: 04afed696f9f14da85a460353645d1f5
+    - path: output/bamtools/versions.yml
+      md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3
+
+- name: bamtools convert test_bamtools_convert_pileup
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.pileup
+      md5sum: e5a3cb4a3e1bf980a575fafce6a2826f
+    - path: output/bamtools/versions.yml
+      md5sum: fd3ad0edd1e085b1a002e0593d1d5814
+
+- name: bamtools convert test_bamtools_convert_sam
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.sam
+      md5sum: 61ab3d0de16a9da8b651f9c692e19d5e
+    - path: output/bamtools/versions.yml
+      md5sum: 4be470ce3cc0143ae5ae415b612a4965
+
+- name: bamtools convert test_bamtools_convert_yaml
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.yaml
+      md5sum: 68b56f198da036fef33e150eb773dc3b
+    - path: output/bamtools/versions.yml
+      md5sum: 1116abc088c5edf11bee393961c18b3e