Add deeptools bamcoverage (#1316)

* Add deeptools bamcoverage

* remove todo string

* Add in when

* fix c&p version format error

* Fix md5sums

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

modules/deeptools/bamcoverage/main.nf

@@ -0,0 +1,37 @@
+process DEEPTOOLS_BAMCOVERAGE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
+        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
+
+    input:
+    tuple val(meta), path(input), path(input_index)
+
+    output:
+    tuple val(meta), path("*.bigWig")   , emit: bigwig, optional: true
+    tuple val(meta), path("*.bedgraph") , emit: bedgraph, 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}.bigWig"
+
+    """
+    bamCoverage \
+    --bam $input \
+    $args \
+    --numberOfProcessors ${task.cpus} \
+    --outFileName ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
+    END_VERSIONS
+    """
+}

modules/deeptools/bamcoverage/meta.yml

@@ -0,0 +1,49 @@
+name: deeptools_bamcoverage
+description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
+keywords:
+  - sort
+tools:
+  - deeptools:
+      description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data
+      homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
+      documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
+      tool_dev_url: https://github.com/deeptools/deepTools/
+      doi: "https://doi.org/10.1093/nar/gkw257"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/CRAM file
+      pattern: "*.{bam,cram}"
+  - input_index:
+      type: file
+      description: BAM/CRAM index file
+      pattern: "*.{bai,crai}"
+
+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"
+  - bigWig:
+      type: file
+      description: BigWig file
+      pattern: "*.bigWig"
+  - bedgraph:
+      type: file
+      description: Bedgraph file
+      pattern: "*.bedgraph"
+
+authors:
+  - "@FriederikeHanssen"

tests/config/pytest_modules.yml

@@ -400,6 +400,10 @@ deeparg/predict:
   - modules/deeparg/predict/**
   - tests/modules/deeparg/predict/**
 
+deeptools/bamcoverage:
+  - modules/deeptools/bamcoverage/**
+  - tests/modules/deeptools/bamcoverage/**
+
 deeptools/computematrix:
   - modules/deeptools/computematrix/**
   - tests/modules/deeptools/computematrix/**

tests/modules/deeptools/bamcoverage/main.nf

@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPTOOLS_BAMCOVERAGE } from '../../../../modules/deeptools/bamcoverage/main.nf'
+
+workflow test_deeptools_bamcoverage_bam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+        ]
+
+    DEEPTOOLS_BAMCOVERAGE ( input )
+}
+
+workflow test_deeptools_bamcoverage_cram {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+        ]
+
+    DEEPTOOLS_BAMCOVERAGE ( input )
+}

tests/modules/deeptools/bamcoverage/nextflow.config

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

tests/modules/deeptools/bamcoverage/test.yml

@@ -0,0 +1,21 @@
+- name: deeptools bamcoverage test_deeptools_bamcoverage_bam
+  command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c tests/config/nextflow.config
+  tags:
+    - deeptools
+    - deeptools/bamcoverage
+  files:
+    - path: output/deeptools/test.bigWig
+      md5sum: 95fe9383a9e6c02aea6b785cf074274f
+    - path: output/deeptools/versions.yml
+      md5sum: 68c94e73b7a8c0935578bad61fea54c1
+
+- name: deeptools bamcoverage test_deeptools_bamcoverage_cram
+  command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c tests/config/nextflow.config
+  tags:
+    - deeptools
+    - deeptools/bamcoverage
+  files:
+    - path: output/deeptools/test.bigWig
+      md5sum: 95fe9383a9e6c02aea6b785cf074274f
+    - path: output/deeptools/versions.yml
+      md5sum: 665bbd2979c49bf3974a24bd44a88e94