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Merge pull request #1624 from nvnieuwk/new-module-rtg/vcfeval
New module rtg/vcfeval
This commit is contained in:
nvnieuwk
GitHub
commit
914e56163a
7 changed files with 394 additions and 83 deletions
59
modules/rtgtools/vcfeval/main.nf
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59
modules/rtgtools/vcfeval/main.nf
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@ -0,0 +1,59 @@
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process RTGTOOLS_VCFEVAL {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0':
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'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(query_vcf), path(query_vcf_tbi)
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tuple path(truth_vcf), path(truth_vcf_tbi)
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path(truth_regions)
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path(evaluation_regions)
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path(sdf)
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output:
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tuple val(meta), path("**results/{done,progress,*.log}") , emit: logs
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tuple val(meta), path("**tp.vcf.gz"), path("**tp.vcf.gz.tbi") , emit: tp
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tuple val(meta), path("**fn.vcf.gz"), path("**fn.vcf.gz.tbi") , emit: fn
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tuple val(meta), path("**fp.vcf.gz"), path("**fp.vcf.gz.tbi") , emit: fp
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tuple val(meta), path("**baseline.vcf.gz"), path("**baseline.vcf.gz.tbi") , emit: baseline
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tuple val(meta), path("**.tsv.gz") , emit: roc
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tuple val(meta), path("**results/summary.txt") , emit: summary
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tuple val(meta), path("**results/phasing.txt") , emit: phasing
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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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script:
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def args = task.ext.args ?: ""
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def prefix = task.ext.prefix ?: "${meta.id}"
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def bed_regions = truth_regions ? "--bed-regions=$truth_regions" : ""
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def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
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def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
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def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
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"""
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$truth_index
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$query_index
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rtg vcfeval \\
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$args \\
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--baseline=$truth_vcf \\
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$bed_regions \\
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$eval_regions \\
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--calls=$query_vcf \\
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--output=${prefix}_results \\
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--template=$sdf \\
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--threads=$task.cpus \\
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
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END_VERSIONS
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"""
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}
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95
modules/rtgtools/vcfeval/meta.yml
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95
modules/rtgtools/vcfeval/meta.yml
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@ -0,0 +1,95 @@
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name: "rtgtools_vcfeval"
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description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set
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keywords:
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- benchmarking
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- vcf
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- rtg-tools
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tools:
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- "rtgtools":
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description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation"
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homepage: "https://www.realtimegenomics.com/products/rtg-tools"
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documentation: "https://github.com/RealTimeGenomics/rtg-tools"
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tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
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doi: ""
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licence: "['BSD']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- truth_vcf:
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type: file
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description: A standard VCF to compare against
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pattern: "*.{vcf,vcf.gz}"
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- truth_vcf_index:
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type: file
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description: The index of the standard VCF (optional)
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pattern: "*.tbi"
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- query_vcf:
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type: file
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description: A VCF with called variants to benchmark against the standard
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pattern: "*.{vcf,vcf.gz}"
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- query_vcf_index:
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type: file
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description: The index of the called VCF (optional)
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pattern: "*.tbi"
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- truth_regions:
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type: file
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description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)
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pattern: "*.bed"
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- evaluation_regions:
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type: file
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description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)
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pattern: "*.bed"
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- sdf:
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type: file
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description: The SDF (RTG Sequence Data File) folder of the reference genome
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pattern: "*"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- logging:
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type: file
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description: Files containing logging from vcfeval
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pattern: "*{done,progress,.log}"
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- tp:
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type: file
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description: A tuple containing the VCF and TBI file for the true positive variants
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pattern: "tp.vcf{.gz,.gz.tbi}"
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- baseline:
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type: file
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description: A tuple containing the VCF and TBI file for the baseline true positive variants
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pattern: "tp-baseline.vcf{.gz,.gz.tbi}"
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- fp:
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type: file
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description: A tuple containing the VCF and TBI file for the false positive variants
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pattern: "fp.vcf{.gz,.gz.tbi}"
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- fn:
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type: file
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description: A tuple containing the VCF and TBI file for the false negative variants
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pattern: "fn.vcf{.gz,.gz.tbi}"
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- roc:
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type: file
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description: TSV files containing ROC data for the evaluated variants
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pattern: "*.tsv.gz"
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- summary:
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type: file
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description: A TXT file containing the summary of the evaluation
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pattern: "summary.txt"
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- phasing:
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type: file
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description: A TXT file containing the data on the phasing
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pattern: "phasing.txt"
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authors:
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- "@nvnieuwk"
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@ -1619,6 +1619,10 @@ rseqc/tin:
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- modules/rseqc/tin/**
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- tests/modules/rseqc/tin/**
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rtgtools/vcfeval:
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- modules/rtgtools/vcfeval/**
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- tests/modules/rtgtools/vcfeval/**
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salmon/index:
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- modules/salmon/index/**
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- tests/modules/salmon/index/**
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@ -135,6 +135,7 @@ params {
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transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
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genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
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genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
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genome_21_sdf = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz"
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genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
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genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
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genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
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@ -212,110 +213,113 @@ params {
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test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
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test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
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test_paired_end_hla_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
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test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
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test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
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test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
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test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
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test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
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test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
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test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
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test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
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test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
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test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
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test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
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test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
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test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
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test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
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test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
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test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
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test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
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test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
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test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
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test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
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test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
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test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
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test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
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test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
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test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
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test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
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mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
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mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
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mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
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mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
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test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
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test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
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test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
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test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
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test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
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test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
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test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
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test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
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test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
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test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
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test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
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test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
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test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
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test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
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test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
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test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
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test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
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test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
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test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
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test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
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test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
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test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
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test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
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test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
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test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
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test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
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test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
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test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
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test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
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test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
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test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
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test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
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test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
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test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
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test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
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test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
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test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
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test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
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test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
|
||||
test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
|
||||
test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
|
||||
test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
|
||||
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
|
||||
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
|
||||
|
||||
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
|
||||
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
|
||||
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
|
||||
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
||||
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
|
||||
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
|
||||
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
|
||||
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
||||
|
||||
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
||||
test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
|
||||
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
||||
test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
|
||||
|
||||
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_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_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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
|
||||
test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
|
||||
test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
|
||||
test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
|
||||
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"
|
||||
|
||||
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
|
||||
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
||||
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
|
||||
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
|
||||
test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
|
||||
test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
|
||||
test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
|
||||
test2_recal = "${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"
|
||||
test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
|
||||
test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
|
||||
test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
|
||||
|
||||
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
|
||||
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
|
||||
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
|
||||
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
|
||||
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
|
||||
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
||||
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
|
||||
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
|
||||
test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
|
||||
test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
|
||||
test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
|
||||
|
||||
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
|
||||
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
|
||||
test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
|
||||
test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
|
||||
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
|
||||
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
|
||||
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
|
||||
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
|
||||
|
||||
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
||||
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
||||
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
|
||||
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
|
||||
test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
|
||||
test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
|
||||
|
||||
test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
|
||||
test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
|
||||
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
||||
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
||||
|
||||
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
||||
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
||||
test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
|
||||
test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
|
||||
|
||||
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
|
||||
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
|
||||
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
||||
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
||||
|
||||
test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
|
||||
test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
|
||||
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
|
||||
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
|
||||
|
||||
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
|
||||
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
|
||||
test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
|
||||
test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
|
||||
|
||||
cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
|
||||
cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
|
||||
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
|
||||
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
|
||||
|
||||
test_rnaseq_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
|
||||
test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
|
||||
cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
|
||||
cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
|
||||
|
||||
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
|
||||
test_rnaseq_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
|
||||
test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
|
||||
|
||||
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
|
||||
}
|
||||
'pacbio' {
|
||||
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
|
||||
|
|
|
|||
69
tests/modules/rtgtools/vcfeval/main.nf
Normal file
69
tests/modules/rtgtools/vcfeval/main.nf
Normal file
|
|
@ -0,0 +1,69 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
|
||||
include { UNTAR } from '../../../modules/untar/main.nf'
|
||||
|
||||
workflow test_rtgtools_vcfeval {
|
||||
|
||||
input = [
|
||||
[ id:'test' ], // meta map
|
||||
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),
|
||||
]
|
||||
|
||||
truth = [
|
||||
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)
|
||||
]
|
||||
|
||||
truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
|
||||
|
||||
evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
|
||||
compressed_sdf = [
|
||||
[],
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
|
||||
]
|
||||
|
||||
sdf = UNTAR( compressed_sdf ).untar
|
||||
.map({
|
||||
meta, folder ->
|
||||
folder
|
||||
})
|
||||
|
||||
|
||||
RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
|
||||
}
|
||||
|
||||
workflow test_rtgtools_vcfeval_no_optional_inputs {
|
||||
|
||||
input = [
|
||||
[ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
|
||||
[],
|
||||
]
|
||||
|
||||
truth = [
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
truth_regions = []
|
||||
|
||||
evaluation_regions = []
|
||||
|
||||
compressed_sdf = [
|
||||
[],
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
|
||||
]
|
||||
|
||||
sdf = UNTAR( compressed_sdf ).untar
|
||||
.map({
|
||||
meta, folder ->
|
||||
[folder]
|
||||
})
|
||||
|
||||
RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
|
||||
}
|
||||
5
tests/modules/rtgtools/vcfeval/nextflow.config
Normal file
5
tests/modules/rtgtools/vcfeval/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
75
tests/modules/rtgtools/vcfeval/test.yml
Normal file
75
tests/modules/rtgtools/vcfeval/test.yml
Normal file
|
|
@ -0,0 +1,75 @@
|
|||
- 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
|
||||
files:
|
||||
- path: output/rtgtools/test_results/done
|
||||
- path: output/rtgtools/test_results/fn.vcf.gz
|
||||
md5sum: be9c9106055bfad4c5985bc0d33efd56
|
||||
- path: output/rtgtools/test_results/fn.vcf.gz.tbi
|
||||
md5sum: 092a7a3162e7cff25d273525751eb284
|
||||
- path: output/rtgtools/test_results/fp.vcf.gz
|
||||
md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
|
||||
- path: output/rtgtools/test_results/fp.vcf.gz.tbi
|
||||
md5sum: 092a7a3162e7cff25d273525751eb284
|
||||
- path: output/rtgtools/test_results/non_snp_roc.tsv.gz
|
||||
md5sum: ad5bad32c48f05aef232e2c0e708877a
|
||||
- path: output/rtgtools/test_results/phasing.txt
|
||||
md5sum: 133677dbd8be657439ea2b03fdfb8795
|
||||
- path: output/rtgtools/test_results/progress
|
||||
- path: output/rtgtools/test_results/snp_roc.tsv.gz
|
||||
md5sum: 6785b83d66486e7e6c75c5a5b1574c09
|
||||
- path: output/rtgtools/test_results/summary.txt
|
||||
md5sum: f4c8df93c8bdab603036bbc27b4a28c3
|
||||
- path: output/rtgtools/test_results/tp-baseline.vcf.gz
|
||||
md5sum: be9c9106055bfad4c5985bc0d33efd56
|
||||
- path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
|
||||
md5sum: 092a7a3162e7cff25d273525751eb284
|
||||
- path: output/rtgtools/test_results/tp.vcf.gz
|
||||
md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
|
||||
- path: output/rtgtools/test_results/tp.vcf.gz.tbi
|
||||
md5sum: 092a7a3162e7cff25d273525751eb284
|
||||
- path: output/rtgtools/test_results/vcfeval.log
|
||||
- path: output/rtgtools/test_results/weighted_roc.tsv.gz
|
||||
md5sum: fa7c046ea0084172f1ef91f19de07b2b
|
||||
- path: output/rtgtools/versions.yml
|
||||
md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
|
||||
|
||||
- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
|
||||
command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
|
||||
tags:
|
||||
- rtgtools
|
||||
- rtgtools/vcfeval
|
||||
files:
|
||||
- path: output/rtgtools/test_results/done
|
||||
- path: output/rtgtools/test_results/fn.vcf.gz
|
||||
md5sum: c11c889a4f42c8ea325748bd768ea34d
|
||||
- path: output/rtgtools/test_results/fn.vcf.gz.tbi
|
||||
md5sum: 092a7a3162e7cff25d273525751eb284
|
||||
- path: output/rtgtools/test_results/fp.vcf.gz
|
||||
md5sum: 138e85c1cd79f8fea9a33e81ce0c734c
|
||||
- path: output/rtgtools/test_results/fp.vcf.gz.tbi
|
||||
md5sum: 092a7a3162e7cff25d273525751eb284
|
||||
- path: output/rtgtools/test_results/non_snp_roc.tsv.gz
|
||||
md5sum: 34fb78a008dfc0bef02807b8a7012b07
|
||||
- path: output/rtgtools/test_results/phasing.txt
|
||||
md5sum: 133677dbd8be657439ea2b03fdfb8795
|
||||
- path: output/rtgtools/test_results/progress
|
||||
- path: output/rtgtools/test_results/snp_roc.tsv.gz
|
||||
md5sum: a4c5761c2653e2d04fc84c1cea13b1f0
|
||||
- path: output/rtgtools/test_results/summary.txt
|
||||
md5sum: f33feb32f84958fb931063044fba369b
|
||||
- path: output/rtgtools/test_results/tp-baseline.vcf.gz
|
||||
md5sum: d1c2d990899edf127ea5fcca8866fcb0
|
||||
- path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
|
||||
md5sum: 3307008fea47adb75c46d395c5567bc0
|
||||
- path: output/rtgtools/test_results/tp.vcf.gz
|
||||
md5sum: e35b4dab82894eee9b77c81f9bc89cca
|
||||
- path: output/rtgtools/test_results/tp.vcf.gz.tbi
|
||||
md5sum: 45d8f8793140944f129e728299918c88
|
||||
- path: output/rtgtools/test_results/vcfeval.log
|
||||
- path: output/rtgtools/test_results/weighted_roc.tsv.gz
|
||||
md5sum: 5b8efc9e9381f604880412800f58e4e9
|
||||
- path: output/rtgtools/versions.yml
|
||||
md5sum: 55568e4bbe5ab7e634a1f392abb89cc4
|
||||
Loading…
Reference in a new issue