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https://github.com/MillironX/nf-core_modules.git
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Merge pull request #1700 from SusiJo/gatk_spark
Fix gatk/markduplicatesspark
This commit is contained in:
commit
c587fd1fe3
5 changed files with 87 additions and 26 deletions
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@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES_SPARK {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0 conda-forge::openjdk=8.0.312" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
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'broadinstitute/gatk:4.2.3.0' }"
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@ -14,8 +14,9 @@ process GATK4_MARKDUPLICATES_SPARK {
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path dict
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output:
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tuple val(meta), path("${prefix}"), emit: output
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path "versions.yml" , emit: versions
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tuple val(meta), path("${prefix}"), emit: output
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tuple val(meta), path("*.metrics"), emit: metrics, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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@ -25,6 +26,7 @@ process GATK4_MARKDUPLICATES_SPARK {
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prefix = task.ext.prefix ?: "${meta.id}"
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def input_list = bam.collect{"--input $it"}.join(' ')
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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@ -32,8 +34,6 @@ process GATK4_MARKDUPLICATES_SPARK {
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avail_mem = task.memory.giga
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}
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"""
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export SPARK_USER=spark3
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gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
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$input_list \\
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--output $prefix \\
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@ -45,6 +45,7 @@ process GATK4_MARKDUPLICATES_SPARK {
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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openjdk: \$(echo \$(java -version 2>&1) | grep version | sed 's/\"//g' | cut -f3 -d ' ')
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END_VERSIONS
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"""
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}
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@ -58,3 +58,4 @@ authors:
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- "@ajodeh-juma"
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- "@FriederikeHanssen"
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- "@maxulysse"
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- "@SusiJo"
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@ -3,26 +3,55 @@
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nextflow.enable.dsl = 2
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include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
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include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
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include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
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workflow test_gatk4_markduplicates_spark {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
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}
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// chr 22
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workflow test_gatk4_markduplicates_spark_multiple_bams {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
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] ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
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}
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// chr 22
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workflow test_gatk4_markduplicates_spark_multiple_bams_cram_out {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
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] ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MARKDUPLICATES_SPARK_CRAM ( input, fasta, fai, dict )
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}
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// chr 22
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workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
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] ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MARKDUPLICATES_SPARK_METRICS ( input, fasta, fai, dict )
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}
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@ -2,4 +2,18 @@ process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: GATK4_MARKDUPLICATES_SPARK {
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ext.prefix = { "${meta.id}.bam" }
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}
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withName: GATK4_MARKDUPLICATES_SPARK_CRAM {
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ext.prefix = { "${meta.id}.cram" }
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}
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withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
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ext.args = '--metrics-file test.metrics'
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ext.prefix = { "${meta.id}.bam" }
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}
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}
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// override tests/config/nextflow.config
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docker.userEmulation = false
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@ -1,25 +1,41 @@
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- name: gatk4 markduplicates test_gatk4_markduplicates_spark
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command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark
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command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicatesspark
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files:
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- path: output/gatk4/test.bai
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md5sum: e9c125e82553209933883b4fe2b8d7c2
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- path: output/gatk4/test.bam
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md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
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- path: output/gatk4/test.metrics
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md5sum: dc1a09ac6371aab7c50d1a554baa06d3
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- path: output/gatk4/versions.yml
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- name: gatk4 markduplicates test_gatk4_markduplicates_spark_multiple_bams
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command: nextflow run tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams
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command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicatesspark
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files:
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- path: output/gatk4/test.bai
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md5sum: bad71df9c876e72a5bc0a3e0fd755f92
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- path: output/gatk4/test.bam
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md5sum: 8187febc6108ffef7f907e89b9c091a4
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- path: output/gatk4/test.metrics
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md5sum: 898cb0a6616897d8ada90bab53bf0837
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- path: output/gatk4/versions.yml
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- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_cram_out
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command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_cram_out -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicatesspark
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files:
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- path: output/gatk4/test.cram
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md5sum: 2271016de5e4199736598f39d12d7587
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- path: output/gatk4/versions.yml
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- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_metrics
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command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_metrics -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicatesspark
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files:
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- path: output/gatk4/test.bam
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md5sum: 898cb0a6616897d8ada90bab53bf0837
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- path: output/gatk4/test.metrics
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contains: ["## METRICS CLASS", "org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics"]
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- path: output/gatk4/versions.yml
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