From 84b354ab6a110861db68e0d3eb6b0e746d014845 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 6 May 2022 14:23:40 +0200 Subject: [PATCH] Added the rtgtools/vcfeval module --- modules/rtgtools/vcfeval/main.nf | 70 ++++++++++--------------- modules/rtgtools/vcfeval/meta.yml | 54 +++++++++++-------- tests/config/test_data.config | 4 ++ tests/modules/rtgtools/vcfeval/main.nf | 32 +++++++++-- tests/modules/rtgtools/vcfeval/test.yml | 29 ++++++---- 5 files changed, 113 insertions(+), 76 deletions(-) diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf index 4fd8aa4b..0b927a22 100644 --- a/modules/rtgtools/vcfeval/main.nf +++ b/modules/rtgtools/vcfeval/main.nf @@ -1,46 +1,18 @@ -// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) -// https://github.com/nf-core/modules/tree/master/modules -// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: -// https://nf-co.re/join -// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. -// All other parameters MUST be provided using the "task.ext" directive, see here: -// https://www.nextflow.io/docs/latest/process.html#ext -// where "task.ext" is a string. -// Any parameters that need to be evaluated in the context of a particular sample -// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. -// TODO nf-core: Software that can be piped together SHOULD be added to separate module files -// unless there is a run-time, storage advantage in implementing in this way -// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: -// bwa mem | samtools view -B -T ref.fasta -// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty -// list (`[]`) instead of a file can be used to work around this issue. - process RTGTOOLS_VCFEVAL { tag "$meta.id" label 'process_medium' - // TODO nf-core: List required Conda package(s). - // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). - // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. - // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': 'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" input: - // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" - // MUST be provided as an input via a Groovy Map called "meta". - // This information may not be required in some instances e.g. indexing reference genome files: - // https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf - // TODO nf-core: Where applicable please provide/convert compressed files as input/output - // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. - tuple val(meta), path(bam) + tuple val(meta), path(truth_vcf), path(truth_vcf_tbi), path(query_vcf), path(query_vcf_tbi), path(bed) + path(sdf) output: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here + tuple val(meta), path("*.txt"), emit: results path "versions.yml" , emit: versions when: @@ -49,19 +21,35 @@ process RTGTOOLS_VCFEVAL { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 - // If the software is unable to output a version number on the command-line then it can be manually specified - // e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf - // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) - // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive - // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter - // using the Nextflow "task" variable e.g. "--threads $task.cpus" - // TODO nf-core: Please replace the example samtools command below with your module's command - // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) + def regions = bed ? "--bed-regions=$bed" : "" + def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf" + def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf" + + sdf_basename = sdf.getBaseName().replace(".tar","") + tar_decomp = "" + if((sdf =~ /.tar.gz\b/).find() == true) { + tar_decomp = "tar -xzf $sdf" + } + """ + $tar_decomp + + $truth_index + $query_index + + rtg vcfeval \\ + $args \\ + --baseline=$truth_vcf \\ + $regions \\ + --calls=$query_vcf \\ + --output=$prefix \\ + --template=$sdf_basename \\ + --threads=$task.cpus \\ + > ${prefix}_results.txt + cat <<-END_VERSIONS > versions.yml "${task.process}": - rtgtools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) + rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) END_VERSIONS """ } diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml index 512a7734..061ea876 100644 --- a/modules/rtgtools/vcfeval/meta.yml +++ b/modules/rtgtools/vcfeval/meta.yml @@ -1,51 +1,63 @@ name: "rtgtools_vcfeval" -## TODO nf-core: Add a description of the module and list keywords -description: write your description here +description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set keywords: - - sort + - benchmarking + - vcf + - rtg-tools tools: - "rtgtools": - ## TODO nf-core: Add a description and other details for the software below description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" - homepage: "None" - documentation: "None" - tool_dev_url: "None" + homepage: "https://www.realtimegenomics.com/products/rtg-tools" + documentation: "https://github.com/RealTimeGenomics/rtg-tools" + tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" doi: "" licence: "['BSD']" -## TODO nf-core: Add a description of all of the variables used as input input: - # Only when we have meta - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - # - ## TODO nf-core: Delete / customise this example input - - bam: + - truth_vcf: type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + description: A standard VCF to compare against + pattern: "*.{vcf,vcf.gz}" + - truth_vcf_index: + type: file + description: The index of the standard VCF (optional) + pattern: "*.tbi" + - query_vcf: + type: file + description: A VCF with called variants to benchmark against the standard + pattern: "*.{vcf,vcf.gz}" + - query_vcf_index: + type: file + description: The index of the called VCF (optional) + pattern: "*.tbi" + - bed: + type: file + description: The BED file of the called VCF + pattern: "*.bed" + - sdf: + type: folder/file + description: The SDF (RTG Sequence Data File) of the reference genome. Can be a folder or a tar-zipped folder. + pattern: "*.{,tar.gz}" -## TODO nf-core: Add a description of all of the variables used as output output: - #Only when we have meta - 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" - ## TODO nf-core: Delete / customise this example output - - bam: + - results: type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + description: A text file containing the results of the benchmark + pattern: "*.txt" authors: - "@nvnieuwk" diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 62e38c4d..5a204ae1 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -132,6 +132,7 @@ params { transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta" genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta" genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz" + genome_21_sdf = "${test_data_dir}/genomics/homo_sapiens/genome/genome_sdf.tar.gz" genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" @@ -263,6 +264,9 @@ params { test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" + test2_haplotc_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" + test2_haplotc_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" + test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" diff --git a/tests/modules/rtgtools/vcfeval/main.nf b/tests/modules/rtgtools/vcfeval/main.nf index 1a4297fc..baf3c54d 100644 --- a/tests/modules/rtgtools/vcfeval/main.nf +++ b/tests/modules/rtgtools/vcfeval/main.nf @@ -7,9 +7,35 @@ include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf' workflow test_rtgtools_vcfeval { input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) ] - RTGTOOLS_VCFEVAL ( input ) + sdf = Channel.value( + file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) + ) + + RTGTOOLS_VCFEVAL ( input, sdf ) +} + +workflow test_rtgtools_vcfeval_no_index { + + input = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), + [], + file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), + [], + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) + ] + + sdf = Channel.value( + file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) + ) + + RTGTOOLS_VCFEVAL ( input, sdf ) } diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml index 862f4acd..73ed8cc6 100644 --- a/tests/modules/rtgtools/vcfeval/test.yml +++ b/tests/modules/rtgtools/vcfeval/test.yml @@ -1,14 +1,21 @@ -## TODO nf-core: Please run the following command to build this file: -# nf-core modules create-test-yml rtgtools/vcfeval -- name: "rtgtools vcfeval" - command: nextflow run ./tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c ./tests/config/nextflow.config -c ./tests/modules/rtgtools/vcfeval/nextflow.config +- name: rtgtools vcfeval test_rtgtools_vcfeval + command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c tests/config/nextflow.config tags: - - "rtgtools" - # - - "rtgtools/vcfeval" - # + - rtgtools + - rtgtools/vcfeval files: - - path: "output/rtgtools/test.bam" - md5sum: e667c7caad0bc4b7ac383fd023c654fc + - path: output/rtgtools/test_results.txt + md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4 - path: output/rtgtools/versions.yml - md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b + md5sum: 270ed7a5a8e347b251eb4aa2198f98e8 + +- name: rtgtools vcfeval test_rtgtools_vcfeval_no_index + command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_index -c tests/config/nextflow.config + tags: + - rtgtools + - rtgtools/vcfeval + files: + - path: output/rtgtools/test_results.txt + md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4 + - path: output/rtgtools/versions.yml + md5sum: 8d0407000988c78fa43fe5cfe3d4449d