feat(bbmap): Initialize pileup.sh

modules/bbmap/pileup/main.nf

@@ -0,0 +1,36 @@
+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: stats
+    tuple val(meta), path("*.hist.txt") , emit: hist
+    path "versions.yml"                 , emit: versions
+
+    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
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - bbmap:
+      ## TODO nf-core: Add a description and other details for the software below
+      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: None
+      doi: ""
+      licence: ['UC-LBL license (see package)']
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+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
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@Emiller88"

tests/config/pytest_modules.yml

@@ -82,6 +82,10 @@ bbmap/index:
   - modules/bbmap/index/**
   - tests/modules/bbmap/index/**
 
+bbmap/pileup:
+  - modules/bbmap/pileup/**
+  - tests/modules/bbmap/pileup/**
+
 bcftools/concat:
   - modules/bcftools/concat/**
   - tests/modules/bcftools/concat/**

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 +1,10 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml bbmap/pileup
+- 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.bam
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc