Merge branch 'gatk3-indelrealigner' into upstream-for-indel

modules/gatk/indelrealigner/main.nf

@@ -0,0 +1,54 @@
+process GATK_INDELREALIGNER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
+        'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
+
+    input:
+    tuple val(meta), path(input), path(index), path(intervals)
+    path(fasta)
+    path(fai)
+    path(dict)
+    path(known_vcf)
+
+    output:
+    tuple val(meta), path("*.bam"), path("*.bai"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def known = known_vcf ? "-known ${known_vcf}" : ""
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK IndelRealigner] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+
+    """
+    gatk3 \\
+        -Xmx${avail_mem}g \\
+        -T IndelRealigner \\
+        -R ${fasta} \\
+        -nt ${task.cpus}
+        -I ${input} \\
+        -targetIntervals ${intervals} \\
+        ${known} \\
+        -o ${prefix}.bam \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk: \$(echo \$(gatk3 --version))
+    END_VERSIONS
+    """
+}

modules/gatk/indelrealigner/meta.yml

@@ -0,0 +1,71 @@
+name: "gatk_indelrealigner"
+description: Performs local realignment around indels to correct for mapping errors
+keywords:
+  - bam
+  - vcf
+  - variant calling
+  - indel
+  - realignment
+tools:
+  - "gatk":
+      description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
+      homepage: "https://gatk.broadinstitute.org/hc/en-us"
+      documentation: "https://github.com/broadinstitute/gatk-docs"
+      licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: Sorted and indexed BAM/CRAM/SAM file
+      pattern: "*.bam"
+  - index:
+      type: file
+      description: BAM index file
+      pattern: "*.bai"
+  - intervals:
+      type: file
+      description: Intervals file created by gatk3 RealignerTargetCreator
+      pattern: "*.{intervals,list}"
+  - fasta:
+      type: file
+      description: Reference file used to generate BAM file
+      pattern: ".{fasta,fa,fna}"
+  - fai:
+      type: file
+      description: Index of reference file used to generate BAM file
+      pattern: ".fai"
+  - dict:
+      type: file
+      description: GATK dict file for reference
+      pattern: ".dict"
+  - known_vcf:
+      type: file
+      description: Optional input VCF file(s) with known indels
+      pattern: ".vcf"
+
+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: Sorted and indexed BAM/CRAM/SAM file with local realignment around variants
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: Output BAM Index file
+      pattern: "*.bai"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -715,6 +715,10 @@ gamma/gamma:
   - modules/gamma/gamma/**
   - tests/modules/gamma/gamma/**
 
+gatk/indelrealigner:
+  - modules/gatk/indelrealigner/**
+  - tests/modules/gatk/indelrealigner/**
+
 gatk/realignertargetcreator:
   - modules/gatk/realignertargetcreator/**
   - tests/modules/gatk/realignertargetcreator/**

tests/modules/gatk/indelrealigner/main.nf

@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'
+
+// TODO add REalignerTargetCrator
+
+
+workflow test_gatk_indelrealigner {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bai'], checkIfExists: true),
+        GATK_REALIGNERTARGETCREATOR.out.intervals
+    ]
+
+    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    GATK_INDELREALIGNER ( input, reference, [] )
+}

tests/modules/gatk/indelrealigner/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.prefix = "${meta.id}.realigned"
+
+}

tests/modules/gatk/indelrealigner/test.yml

@@ -0,0 +1,14 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml gatk/indelrealigner
+- name: "gatk indelrealigner"
+  command: nextflow run ./tests/modules/gatk/indelrealigner -entry test_gatk_indelrealigner -c ./tests/config/nextflow.config -c ./tests/modules/gatk/indelrealigner/nextflow.config
+  tags:
+    - "gatk"
+    #
+    - "gatk/indelrealigner"
+    #
+  files:
+    - path: "output/gatk/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/gatk/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b