feat(bbmap): Initialize pileup module (#1441)

* feat(bbmap): Initialize pileup module

* test(bbmap): Update outputs

* test(bbmap): Add pileup tags

* style(bbmap): Add in when

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

modules/bbmap/pileup/main.nf

@@ -0,0 +1,39 @@
+process BBMAP_PILEUP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
+        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.stats.txt"), emit: covstats
+    tuple val(meta), path("*.hist.txt") , emit: hist
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    pileup.sh \\
+        -Xmx${task.memory.toGiga()}g \\
+        in=${bam} \\
+        out=${prefix}.coverage.stats.txt \\
+        hist=${prefix}.coverage.hist.txt \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bbmap: \$(bbversion.sh)
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+}

modules/bbmap/pileup/meta.yml

@@ -0,0 +1,47 @@
+name: "bbmap_pileup"
+description: Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.
+keywords:
+  - fasta
+  - genome
+  - coverage
+tools:
+  - bbmap:
+      description: BBMap is a short read aligner, as well as various other bioinformatic tools.
+      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh"
+      doi: ""
+      licence: ["UC-LBL license (see package)"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: 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 ]
+  - stats:
+      type: file
+      description: Per-scaffold coverage info
+      pattern: "*.stats.txt"
+  - hist:
+      type: file
+      description: "Histogram of # occurrences of each depth level"
+      pattern: "*.hist.txt"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@Emiller88"

tests/config/pytest_modules.yml

@@ -106,6 +106,10 @@ bbmap/index:
   - modules/bbmap/index/**
   - tests/modules/bbmap/index/**
 
+bbmap/pileup:
+  - modules/bbmap/pileup/**
+  - tests/modules/bbmap/pileup/**
+
 bcftools/annotate:
   - modules/bcftools/annotate/**
   - tests/modules/bcftools/annotate/**

tests/modules/bbmap/pileup/main.nf

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

tests/modules/bbmap/pileup/nextflow.config

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

tests/modules/bbmap/pileup/test.yml

@@ -0,0 +1,12 @@
+- name: "bbmap pileup"
+  command: nextflow run ./tests/modules/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/pileup/nextflow.config
+  tags:
+    - "bbmap"
+    - "bbmap/pileup"
+  files:
+    - path: "output/bbmap/test.coverage.stats.txt"
+      md5sum: c3fc9d0681589b69e3301ca3cb27b7a4
+    - path: "output/bbmap/test.coverage.hist.txt"
+      md5sum: 96915920ef42ddc9483457dd4585a088
+    - path: output/bbmap/versions.yml
+      md5sum: 894acc38bdc167dc22851df15e5a8453