diff --git a/modules/gatk4/cnnscorevariants/main.nf b/modules/gatk4/cnnscorevariants/main.nf new file mode 100644 index 00000000..c02c6035 --- /dev/null +++ b/modules/gatk4/cnnscorevariants/main.nf @@ -0,0 +1,57 @@ +process GATK4_CNNSCOREVARIANTS { + tag "$meta.id" + label 'process_low' + + //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 + if (params.enable_conda) { + exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers." + } + container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package + + input: + tuple val(meta), path(vcf), path(aligned_input), path(intervals) + path fasta + path fai + path dict + path architecture + path weights + + output: + tuple val(meta), path("*.vcf.gz"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def aligned_input = aligned_input ? "--input $aligned_input" : "" + def interval_command = intervals ? "--intervals $intervals" : "" + def architecture = architecture ? "--architecture $architecture" : "" + def weights = weights ? "--weights $weights" : "" + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK CnnScoreVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\ + --variant $vcf \\ + --output ${prefix}.vcf.gz \\ + --reference $fasta \\ + $interval_command \\ + $aligned_input \\ + $architecture \\ + $weights \\ + --tmp-dir . \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/cnnscorevariants/meta.yml b/modules/gatk4/cnnscorevariants/meta.yml new file mode 100644 index 00000000..1d47e6e7 --- /dev/null +++ b/modules/gatk4/cnnscorevariants/meta.yml @@ -0,0 +1,72 @@ +name: "gatk4_cnnscorevariants" +description: Apply a Convolutional Neural Net to filter annotated variants +keywords: + - gatk4_cnnscorevariants + - gatk4 + - variants +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: VCF file + pattern: "*.vcf.gz" + - aligned_input: + type: file + description: BAM/CRAM file from alignment (optional) + pattern: "*.{bam,cram}" + - 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" + - architecture: + type: file + description: Neural Net architecture configuration json file (optional) + pattern: "*.json" + - weights: + type: file + description: Keras model HD5 file with neural net weights. (optional) + pattern: "*.hd5" + +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: Annotated VCF file + pattern: "*.vcf" + +authors: + - "@FriederikeHanssen" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 2d0d3226..16411798 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -731,6 +731,10 @@ gatk4/calculatecontamination: - modules/gatk4/calculatecontamination/** - tests/modules/gatk4/calculatecontamination/** +gatk4/cnnscorevariants: + - modules/gatk4/cnnscorevariants/** + - tests/modules/gatk4/cnnscorevariants/** + gatk4/combinegvcfs: - modules/gatk4/combinegvcfs/** - tests/modules/gatk4/combinegvcfs/** diff --git a/tests/modules/gatk4/cnnscorevariants/main.nf b/tests/modules/gatk4/cnnscorevariants/main.nf new file mode 100644 index 00000000..d03acb78 --- /dev/null +++ b/tests/modules/gatk4/cnnscorevariants/main.nf @@ -0,0 +1,18 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf' + +workflow test_gatk4_cnnscorevariants { + + input = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true), + [], + [] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + GATK4_CNNSCOREVARIANTS ( input, fasta, fai, dict, [], [] ) +} diff --git a/tests/modules/gatk4/cnnscorevariants/nextflow.config b/tests/modules/gatk4/cnnscorevariants/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/gatk4/cnnscorevariants/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/gatk4/cnnscorevariants/test.yml b/tests/modules/gatk4/cnnscorevariants/test.yml new file mode 100644 index 00000000..2cbbf5fa --- /dev/null +++ b/tests/modules/gatk4/cnnscorevariants/test.yml @@ -0,0 +1,9 @@ +- name: gatk4 cnnscorevariants test_gatk4_cnnscorevariants + command: nextflow run ./tests/modules/gatk4/cnnscorevariants -entry test_gatk4_cnnscorevariants -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/cnnscorevariants/nextflow.config + tags: + - gatk4 + - gatk4/cnnscorevariants + files: + - path: output/gatk4/test.vcf.gz + contains: + - "##ALT=