Add module: gatk4/leftalignandtrimvariants (#1808)

* Added: gatk4/leftalignandtrimvariants

Additions:
 - GATK4/LeftAlignAndTrimVariants module
 - Use sars-ncov2 test data as this normalises a larger INDEL correctly.

Fixes #1801

* fixup: Added index to output spec

* fixup: Pattern of tbi output corrected to 'tbi'

* gatk4/leftalignandtrimvariants: Added intervals

Changes:
 - gatk4/leftalignandtrimvariants now supports optional interval as BED
 file
 - Tests added with and without interval. Not test BED file excludes all
 variants so no variants are actually normalised.

Fixes #1801

* fixup: leftalignandtrimvariants vcf->tbi fix

* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml

modules/gatk4/leftalignandtrimvariants/main.nf

@@ -0,0 +1,48 @@
+process GATK4_LEFTALIGNANDTRIMVARIANTS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi), path(intervals)
+    path  fasta
+    path  fai
+    path  dict
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    tuple val(meta), path("*.tbi")   , emit: tbi
+    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 interval_command = intervals       ? "--intervals $intervals" : ""
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK LeftAlignAndTrimVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.toGiga()
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}G" LeftAlignAndTrimVariants \\
+        $interval_command \\
+        --variant $vcf \\
+        --output ${prefix}.vcf.gz \\
+        --reference $fasta \\
+        --tmp-dir . \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/leftalignandtrimvariants/meta.yml

@@ -0,0 +1,69 @@
+name: "gatk4_leftalignandtrimvariants"
+description: Left align and trim variants using GATK4 LeftAlignAndTrimVariants.
+keywords:
+  - normalize
+  - norm
+  - vcf
+tools:
+  - gatk4:
+    description: |
+      Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+      with a primary focus on variant discovery and genotyping. Its powerful processing engine
+      and high-performance computing features make it capable of taking on projects of any size.
+    homepage: https://gatk.broadinstitute.org/hc/en-us
+    documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+    doi: 10.1158/1538-7445.AM2017-3590
+    licence: ["Apache-2.0"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: |
+        The vcf file to be normalized
+        e.g. 'file1.vcf.gz'
+  - tbi:
+      type: file
+      description: |
+        Index of the vcf file to be normalized
+        e.g. 'file1.vcf.gz.tbi'
+  - intervals:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "*.fasta.fai"
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+      pattern: "*.dict"
+
+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"
+  - vcf:
+      type: file
+      description: VCF normalized output file
+      pattern: "*.{vcf.gz}"
+  - tbi:
+      type: file
+      description: Tbi index for VCF file
+      pattern: "*.tbi"
+authors:
+  - "@adamrtalbot"

tests/config/pytest_modules.yml

@@ -863,6 +863,10 @@ gatk4/learnreadorientationmodel:
   - modules/gatk4/learnreadorientationmodel/**
   - tests/modules/gatk4/learnreadorientationmodel/**
 
+gatk4/leftalignandtrimvariants:
+  - modules/gatk4/leftalignandtrimvariants/**
+  - tests/modules/gatk4/leftalignandtrimvariants/**
+
 gatk4/markduplicates:
   - modules/gatk4/markduplicates/**
   - tests/modules/gatk4/markduplicates/**

tests/modules/gatk4/leftalignandtrimvariants/main.nf

@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../modules/gatk4/leftalignandtrimvariants/main.nf'
+
+workflow test_gatk4_leftalignandtrimvariants_interval {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_leftalignandtrimvariants_no_interval {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        []
+    ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
+}

tests/modules/gatk4/leftalignandtrimvariants/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'GATK4_LEFTALIGNANDTRIMVARIANTS' {
+        ext.args   = "--split-multi-allelics --dont-trim-alleles --keep-original-ac"
+        ext.prefix = { "${meta.id}.normalised" }
+    }
+}

tests/modules/gatk4/leftalignandtrimvariants/test.yml

@@ -0,0 +1,22 @@
+- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_interval
+  command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_interval -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/leftalignandtrimvariants
+  files:
+    - path: output/gatk4/test.normalised.vcf.gz
+      contains:
+        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
+    - path: output/gatk4/test.normalised.vcf.gz.tbi
+
+- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_no_interval
+  command: nextflow run ./tests/modules/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_no_interval -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/leftalignandtrimvariants/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/leftalignandtrimvariants
+  files:
+    - path: output/gatk4/test.normalised.vcf.gz
+      contains:
+        - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
+        - "MT192765.1\t10502\t.\tTAGATTATGACTGTGTCTCTTTTTGTTACATGCACCA\tTAGAT"
+    - path: output/gatk4/test.normalised.vcf.gz.tbi