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adding new module gatk4_concordance (#9247)
* adding new module gatk4_concordance * fix lint issues * Update modules/nf-core/gatk4/concordance/main.nf Co-authored-by: Simon Pearce <[email protected]> --------- Co-authored-by: Simon Pearce <[email protected]>
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‎modules/nf-core/gatk4/concordance/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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# renovate: datasource=conda depName=bioconda/gatk4
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- bioconda::gatk4=4.6.2.0
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# renovate: datasource=conda depName=bioconda/gcnvkernel
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- bioconda::gcnvkernel=0.9

‎modules/nf-core/gatk4/concordance/main.nf‎

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process GATK4_CONCORDANCE {
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tag "${meta.id}"
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label 'process_low'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data'
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: 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}"
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input:
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tuple val(meta), path(vcf), path(vcf_tbi), path(truth), path(truth_tbi)
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tuple val(meta2), path(intervals)
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tuple val(meta3), path(fasta)
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tuple val(meta4), path(fai)
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tuple val(meta5), path(dict)
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output:
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tuple val(meta), path('*.tsv'), emit: summary
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tuple val(meta), path("*.tpfn.vcf"), emit: tpfn
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tuple val(meta), path("*.tpfp.vcf"), emit: tpfp
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def bed = intervals ? "--intervals $intervals" : ""
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def avail_mem = 3072
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if (!task.memory) {
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log.info('[GATK Concordance] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.')
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}
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else {
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avail_mem = (task.memory.mega * 0.8).intValue()
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}
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"""
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gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
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Concordance \\
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-R $fasta \\
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-eval $vcf \\
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--truth $truth \\
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--summary ${prefix}.summary.tsv \\
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-tpfn ${prefix}.tpfn.vcf \\
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-tpfp ${prefix}.tpfp.vcf \\
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$bed \\
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--tmp-dir . \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.summary.tsv
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touch ${prefix}.tpfp.vcf
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touch ${prefix}.tpfn.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}

‎modules/nf-core/gatk4/concordance/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "gatk4_concordance"
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description: Evaluate concordance of an input VCF against a validated truth VCF
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keywords:
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- concordance
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- gatk4
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- gatk
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- genomics
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- variant calling
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- genotyping
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- vcf
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- comparison
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tools:
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- "gatk4":
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description: "Genome Analysis Toolkit (GATK4)"
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homepage: "https://gatk.broadinstitute.org/hc/en-us"
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documentation: "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s"
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tool_dev_url: "https://github.com/broadinstitute/gatk"
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doi: "10.1158/1538-7445.AM2017-3590"
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licence: ["BSD-3-clause"]
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identifier: "biotools:gatk"
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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:'sample1' ]`
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- vcf:
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type: file
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description: Evaluation VCF file created with a variant caller
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pattern: "*.vcf.gz"
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ontologies:
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- edam: "http://edamontology.org/format_3016"
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- edam: http://edamontology.org/format_3989 # GZIP format
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- vcf_tbi:
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type: file
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description: Index file for the evaluation VCF
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pattern: "*.vcf.gz.tbi"
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ontologies:
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- edam: "http://edamontology.org/format_3616"
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- truth:
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type: file
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description: Truth VCF file created with a variant caller
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pattern: "*.vcf.gz"
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ontologies:
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- edam: "http://edamontology.org/format_3016"
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- edam: http://edamontology.org/format_3989 # GZIP format
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- truth_tbi:
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type: file
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description: Index file for the truth VCF
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pattern: "*.vcf.gz.tbi"
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ontologies:
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- edam: "http://edamontology.org/format_3616"
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- - meta2:
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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:'bed' ]`
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library
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(optional)
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pattern: "*.bed"
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ontologies:
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- edam: "http://edamontology.org/format_3003"
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- - meta3:
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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:'fasta' ]`
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- fasta:
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type: file
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description: Reference FASTA file
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pattern: "*.{fasta,fa}"
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ontologies:
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- edam: "http://edamontology.org/format_1929"
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- - meta4:
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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:'fai' ]`
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- fai:
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type: file
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description: Index of the reference FASTA file
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pattern: "*.fai"
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ontologies:
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- edam: "http://edamontology.org/format_2330"
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- - meta5:
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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:'dict' ]`
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- dict:
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type: file
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description: Sequence dictionary of the reference FASTA file
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pattern: "*.dict"
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ontologies:
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- edam: "http://edamontology.org/format_2330"
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output:
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summary:
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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:'sample1' ]`
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- "*.tsv":
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type: file
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description: A tab-delimited file containing the metrics with number of
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TPs, FPs, FNs, Precision, Recall and F1 statistics
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pattern: "*.tsv"
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ontologies:
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- edam: "http://edamontology.org/format_3475"
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tpfn:
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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:'sample1' ]`
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- "*.tpfn.vcf":
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type: file
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description: Eval VCF file with tagged with TP or FN in "INFO/STATUS"
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pattern: "*.vcf"
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ontologies:
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- edam: "http://edamontology.org/format_3989"
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tpfp:
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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:'sample1' ]`
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- "*.tpfp.vcf":
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type: file
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description: Eval VCF file with tagged with TP or FP in "INFO/STATUS"
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pattern: "*.vcf"
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ontologies:
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- edam: "http://edamontology.org/format_3989"
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versions:
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- versions.yml:
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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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ontologies:
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- edam: "http://edamontology.org/format_3750"
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authors:
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- "@kubranarci"
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maintainers:
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- "@kubranarci"

‎modules/nf-core/gatk4/concordance/tests/main.nf.test‎

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nextflow_process {
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name "Test Process GATK4_CONCORDANCE"
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script "../main.nf"
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process "GATK4_CONCORDANCE"
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tag "modules"
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tag "modules_nfcore"
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tag "gatk4"
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tag "gatk4/concordance"
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test("homo_sapiens - illumina - vcf") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true)
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]
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input[1] = [
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[ id:'bed' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
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]
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input[2] = [
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[ id:'fasta' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
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]
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input[3] = [
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[ id:'fai' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
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]
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input[4] = [
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[ id:'dict' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("homo_sapiens - illumina - vcf - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true)
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]
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input[1] = [
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[ id:'bed' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
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]
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input[2] = [
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[ id:'fasta' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
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]
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input[3] = [
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[ id:'fai' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
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]
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input[4] = [
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[ id:'dict' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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}

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