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Merge branch 'nf-core:master' into cnvkit_bam
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57
modules/gatk4/cnnscorevariants/main.nf
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57
modules/gatk4/cnnscorevariants/main.nf
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process GATK4_CNNSCOREVARIANTS {
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tag "$meta.id"
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label 'process_low'
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//Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers."
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}
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container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package
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input:
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tuple val(meta), path(vcf), path(aligned_input), path(intervals)
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path fasta
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path fai
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path dict
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path architecture
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path weights
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def aligned_input = aligned_input ? "--input $aligned_input" : ""
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def interval_command = intervals ? "--intervals $intervals" : ""
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def architecture = architecture ? "--architecture $architecture" : ""
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def weights = weights ? "--weights $weights" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK CnnScoreVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\
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--variant $vcf \\
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--output ${prefix}.vcf.gz \\
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--reference $fasta \\
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$interval_command \\
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$aligned_input \\
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$architecture \\
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$weights \\
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--tmp-dir . \\
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$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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}
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72
modules/gatk4/cnnscorevariants/meta.yml
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72
modules/gatk4/cnnscorevariants/meta.yml
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name: "gatk4_cnnscorevariants"
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description: Apply a Convolutional Neural Net to filter annotated variants
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keywords:
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- gatk4_cnnscorevariants
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- gatk4
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- variants
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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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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doi: 10.1158/1538-7445.AM2017-3590
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licence: ["Apache-2.0"]
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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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- vcf:
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type: file
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description: VCF file
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pattern: "*.vcf.gz"
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- aligned_input:
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type: file
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description: BAM/CRAM file from alignment (optional)
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pattern: "*.{bam,cram}"
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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 (optional)
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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- architecture:
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type: file
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description: Neural Net architecture configuration json file (optional)
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pattern: "*.json"
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- weights:
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type: file
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description: Keras model HD5 file with neural net weights. (optional)
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pattern: "*.hd5"
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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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- vcf:
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type: file
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description: Annotated VCF file
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pattern: "*.vcf"
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authors:
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- "@FriederikeHanssen"
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@ -731,6 +731,10 @@ gatk4/calculatecontamination:
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- modules/gatk4/calculatecontamination/**
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- tests/modules/gatk4/calculatecontamination/**
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gatk4/cnnscorevariants:
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- modules/gatk4/cnnscorevariants/**
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- tests/modules/gatk4/cnnscorevariants/**
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gatk4/combinegvcfs:
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- modules/gatk4/combinegvcfs/**
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- tests/modules/gatk4/combinegvcfs/**
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18
tests/modules/gatk4/cnnscorevariants/main.nf
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18
tests/modules/gatk4/cnnscorevariants/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf'
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workflow test_gatk4_cnnscorevariants {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
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[],
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_CNNSCOREVARIANTS ( input, fasta, fai, dict, [], [] )
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}
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5
tests/modules/gatk4/cnnscorevariants/nextflow.config
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5
tests/modules/gatk4/cnnscorevariants/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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9
tests/modules/gatk4/cnnscorevariants/test.yml
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9
tests/modules/gatk4/cnnscorevariants/test.yml
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- name: gatk4 cnnscorevariants test_gatk4_cnnscorevariants
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command: nextflow run ./tests/modules/gatk4/cnnscorevariants -entry test_gatk4_cnnscorevariants -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/cnnscorevariants/nextflow.config
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tags:
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- gatk4
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- gatk4/cnnscorevariants
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files:
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- path: output/gatk4/test.vcf.gz
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contains:
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- "##ALT=<ID=NON_REF,Description="
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