Picard addorreplacereadgroups (#1305)

* add picard-addorreplacereadgroups

* add picard_addorreplacereadgroups

* add new line to main.nf

* remove trailing whitespaces

* remove trailing whitespaces

* change to output in test yml

* add when directive

* picard 2.26.10 -> 2.26.9

* picard 2.26.10 -> 2.26.9 test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

modules/picard/addorreplacereadgroups/main.nf

@@ -0,0 +1,53 @@
+process PICARD_ADDORREPLACEREADGROUPS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args        ?: ''
+    def prefix = task.ext.prefix    ?: "${meta.id}"
+    def ID = task.ext.id            ?: "id"
+    def LIBRARY= task.ext.library   ?: "library"
+    def PLATFORM= task.ext.platform ?: "illumina"
+    def BARCODE= task.ext.barcode   ?: "barcode"
+    def SAMPLE= task.ext.sample     ?: "sample"
+    def INDEX= task.ext.index       ?: "index"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        AddOrReplaceReadGroups \\
+        -Xmx${avail_mem}g \\
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam \\
+        -ID ${ID} \\
+        -LB ${LIBRARY} \\
+        -PL ${PLATFORM} \\
+        -PU ${BARCODE} \\
+        -SM ${SAMPLE} \\
+        -CREATE_INDEX true
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/addorreplacereadgroups/meta.yml

@@ -0,0 +1,46 @@
+name: picard_addorreplacereadgroups
+description: Assigns all the reads in a file to a single new read-group
+keywords:
+  - add
+  - replace
+  - read-group
+tools:
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-
+      tool_dev_url: https://github.com/broadinstitute/picard
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Input 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"
+  - bam:
+      type: file
+      description: Output BAM file
+      pattern: "*.{bam}"
+
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"

tests/config/pytest_modules.yml

@@ -1157,6 +1157,10 @@ phyloflash:
   - modules/phyloflash/**
   - tests/modules/phyloflash/**
 
+picard/addorreplacereadgroups:
+  - modules/picard/addorreplacereadgroups/**
+  - tests/modules/picard/addorreplacereadgroups/**
+
 picard/cleansam:
   - modules/picard/cleansam/**
   - tests/modules/picard/cleansam/**

tests/modules/picard/addorreplacereadgroups/main.nf

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

tests/modules/picard/addorreplacereadgroups/nextflow.config

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

tests/modules/picard/addorreplacereadgroups/test.yml

@@ -0,0 +1,10 @@
+- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups
+  command: nextflow run tests/modules/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard/addorreplacereadgroups
+  files:
+    - path: output/picard/test.bam
+      md5sum: 7b82f3461c2d80fc6a10385e78c9427f
+    - path: output/picard/versions.yml
+      md5sum: 8a2d176295e1343146ea433c79bb517f