Merge pull request #1667 from matthdsm/biobambam/bammerge

modules/biobambam/bammerge/main.nf

@@ -0,0 +1,38 @@
+process BIOBAMBAM_BAMMERGE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1':
+        'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("${prefix}.bam")  ,emit: bam
+    tuple val(meta), path("*.bai")          ,optional:true, emit: bam_index
+    tuple val(meta), path("*.md5")          ,optional:true, emit: checksum
+    path "versions.yml"                     ,emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def input_string = bam.join(" I=")
+
+    """
+    bammerge \\
+        I=${input_string} \\
+        $args \\
+        > ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bammerge: \$( bammerge --version |& sed '1!d; s/.*version //; s/.\$//' )
+    END_VERSIONS
+    """
+}

modules/biobambam/bammerge/meta.yml

@@ -0,0 +1,46 @@
+name: biobambam_bammerge
+description: Merge a list of sorted bam files
+keywords:
+  - merge
+  - bam
+tools:
+  - biobambam:
+      description: |
+        biobambam is a set of tools for early stage alignment file processing.
+      homepage: https://gitlab.com/german.tischler/biobambam2
+      documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
+      doi: 10.1186/1751-0473-9-13
+      licence: ["GPL v3"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: List containing 1 or more bam files
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Merged BAM file
+      pattern: "*.bam"
+  - bam_index:
+      type: file
+      description: BAM index file
+      pattern: "*"
+  - checksum:
+      type: file
+      description: Checksum file
+      pattern: "*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@matthdsm"

tests/config/nextflow.config

@@ -19,6 +19,7 @@ if ("$PROFILE" == "singularity") {
 } else {
     docker.enabled = true
     docker.userEmulation = true
+    docker.runOptions = "--platform linux/x86_64"
 }
 
 // Increase time available to build Conda environment

tests/config/pytest_modules.yml

@@ -234,6 +234,10 @@ biobambam/bammarkduplicates2:
   - modules/biobambam/bammarkduplicates2/**
   - tests/modules/biobambam/bammarkduplicates2/**
 
+biobambam/bammerge:
+  - modules/biobambam/bammerge/**
+  - tests/modules/biobambam/bammerge/**
+
 biobambam/bamsormadup:
   - modules/biobambam/bamsormadup/**
   - tests/modules/biobambam/bamsormadup/**

tests/modules/biobambam/bammerge/main.nf

@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BIOBAMBAM_BAMMERGE } from '../../../../modules/biobambam/bammerge/main.nf'
+
+workflow test_biobambam_bammerge_paired {
+
+    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']['test2_paired_end_sorted_bam'], checkIfExists: true)
+        ]
+    ]
+
+    BIOBAMBAM_BAMMERGE ( input )
+}
+
+workflow test_biobambam_bammerge_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+        ]
+    ]
+
+    BIOBAMBAM_BAMMERGE ( input )
+}

tests/modules/biobambam/bammerge/nextflow.config

@@ -0,0 +1,13 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: BIOBAMBAM_BAMMERGE {
+        ext.args = {[
+            "md5=1",
+            "md5filename=${meta.id}.md5",
+            "index=1",
+            "indexfilename=${meta.id}.bam.bai"
+        ].join(" ").trim()}
+    }
+
+}

tests/modules/biobambam/bammerge/test.yml

@@ -0,0 +1,25 @@
+- name: biobambam bammerge test_biobambam_bammerge_paired
+  command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_paired -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bammerge/nextflow.config
+  tags:
+    - biobambam/bammerge
+    - biobambam
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: bc3d32ab6a54d1894ca7cc79387dec57
+    - path: output/biobambam/test.bam.bai
+      md5sum: b8ae542a37a73d79de1c15c765207c53
+    - path: output/biobambam/test.md5
+      md5sum: 31c59857990ceb392242136429e30243
+
+- name: biobambam bammerge test_biobambam_bammerge_single
+  command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config  -c ./tests/modules/biobambam/bammerge/nextflow.config
+  tags:
+    - biobambam/bammerge
+    - biobambam
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 86185d3d6895a7722d3b3a09c6f91bfc
+    - path: output/biobambam/test.bam.bai
+      md5sum: 973680feb6bc73cd1051ea83c7219418
+    - path: output/biobambam/test.md5
+      md5sum: 244a9d1cbc6d74724285c80220e5e427