diff --git a/modules/gatk4/cnnscorevariants/main.nf b/modules/gatk4/cnnscorevariants/main.nf index c02c6035..a1bb3811 100644 --- a/modules/gatk4/cnnscorevariants/main.nf +++ b/modules/gatk4/cnnscorevariants/main.nf @@ -9,7 +9,7 @@ process GATK4_CNNSCOREVARIANTS { container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package input: - tuple val(meta), path(vcf), path(aligned_input), path(intervals) + tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals) path fasta path fai path dict @@ -17,8 +17,9 @@ process GATK4_CNNSCOREVARIANTS { path weights output: - tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*cnn.vcf.gz") , emit: vcf + tuple val(meta), path("*cnn.vcf.gz.tbi"), emit: tbi + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -40,7 +41,7 @@ process GATK4_CNNSCOREVARIANTS { """ gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\ --variant $vcf \\ - --output ${prefix}.vcf.gz \\ + --output ${prefix}.cnn.vcf.gz \\ --reference $fasta \\ $interval_command \\ $aligned_input \\ diff --git a/modules/gatk4/cnnscorevariants/meta.yml b/modules/gatk4/cnnscorevariants/meta.yml index 1d47e6e7..4e59cb8e 100644 --- a/modules/gatk4/cnnscorevariants/meta.yml +++ b/modules/gatk4/cnnscorevariants/meta.yml @@ -25,6 +25,10 @@ input: type: file description: VCF file pattern: "*.vcf.gz" + - tbi: + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" - aligned_input: type: file description: BAM/CRAM file from alignment (optional) @@ -67,6 +71,10 @@ output: type: file description: Annotated VCF file pattern: "*.vcf" + - tbi: + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" authors: - "@FriederikeHanssen" diff --git a/modules/gatk4/filtervarianttranches/main.nf b/modules/gatk4/filtervarianttranches/main.nf new file mode 100644 index 00000000..98e620e7 --- /dev/null +++ b/modules/gatk4/filtervarianttranches/main.nf @@ -0,0 +1,51 @@ +process GATK4_FILTERVARIANTTRANCHES { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + + input: + tuple val(meta), path(vcf), path(tbi), path(intervals) + path resources + path resources_index + path fasta + path fai + path dict + + + output: + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def resources = resources.collect{"--resource $it"}.join(' ') + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK FilterVariantTranches] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + gatk --java-options "-Xmx${avail_mem}g" FilterVariantTranches \\ + --variant $vcf \\ + $resources \\ + --output ${prefix}.filtered.vcf.gz \\ + --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/filtervarianttranches/meta.yml b/modules/gatk4/filtervarianttranches/meta.yml new file mode 100644 index 00000000..f89063a5 --- /dev/null +++ b/modules/gatk4/filtervarianttranches/meta.yml @@ -0,0 +1,68 @@ +name: "gatk4_filtervarianttranches" +description: Apply tranche filtering +keywords: + - gatk4 + - filtervarianttranches + +tools: + - "gatk4": + description: Genome Analysis Toolkit (GATK4) + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us + tool_dev_url: https://github.com/broadinstitute/gatk + doi: "10.1158/1538-7445.AM2017-3590" + licence: ["BSD-3-clause"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: a VCF file containing variants, must have info key:CNN_2D + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file matching with -vcf + pattern: "*.vcf.gz.tbi" + - resources: + type: list + description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary + pattern: "*.vcf.gz" + - resources_index: + type: list + description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary + pattern: "*.vcf.gz" + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - 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 file + pattern: "*.vcf.gz" + - tbi: + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" + +authors: + - "@FriederikeHanssen" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index c1aeb0c6..78e85487 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -759,6 +759,10 @@ gatk4/filtermutectcalls: - modules/gatk4/filtermutectcalls/** - tests/modules/gatk4/filtermutectcalls/** +gatk4/filtervarianttranches: + - modules/gatk4/filtervarianttranches/** + - tests/modules/gatk4/filtervarianttranches/** + gatk4/gatherbqsrreports: - modules/gatk4/gatherbqsrreports/** - tests/modules/gatk4/gatherbqsrreports/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 5937e869..cf7d45f6 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -266,6 +266,8 @@ params { test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" + test_haplotc_cnn_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz" + test_haplotc_cnn_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi" test2_haplotc_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" test2_haplotc_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" diff --git a/tests/modules/gatk4/cnnscorevariants/main.nf b/tests/modules/gatk4/cnnscorevariants/main.nf index d03acb78..1654c54a 100644 --- a/tests/modules/gatk4/cnnscorevariants/main.nf +++ b/tests/modules/gatk4/cnnscorevariants/main.nf @@ -7,7 +7,8 @@ include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevaria workflow test_gatk4_cnnscorevariants { input = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), [], [] ] diff --git a/tests/modules/gatk4/cnnscorevariants/test.yml b/tests/modules/gatk4/cnnscorevariants/test.yml index 2cbbf5fa..eb2e681f 100644 --- a/tests/modules/gatk4/cnnscorevariants/test.yml +++ b/tests/modules/gatk4/cnnscorevariants/test.yml @@ -1,9 +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 + - gatk4 files: - - path: output/gatk4/test.vcf.gz - contains: - - "##ALT=