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Merge pull request #1714 from nvnieuwk/new-module-gatk4/ComposeSTRTableFile
added gatk4/composestrtablefile
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commit
95e8afe627
6 changed files with 128 additions and 0 deletions
53
modules/gatk4/composestrtablefile/main.nf
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53
modules/gatk4/composestrtablefile/main.nf
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process GATK4_COMPOSESTRTABLEFILE {
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tag "$fasta"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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path(fasta)
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path(fasta_fai)
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path(dict)
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output:
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path "*.zip" , emit: str_table
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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 avail_mem = 6
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if (!task.memory) {
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log.info '[GATK ComposeSTRTableFile] Available memory not known - defaulting to 6GB. 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" ComposeSTRTableFile \\
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--reference $fasta \\
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--output ${fasta.baseName}.zip \\
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--tmp-dir . \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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"""
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touch test.zip
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cat <<-END_VERSIONS > versions.yml
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"${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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43
modules/gatk4/composestrtablefile/meta.yml
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43
modules/gatk4/composestrtablefile/meta.yml
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name: "gatk4_composestrtablefile"
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description: This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.
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keywords:
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- gatk4
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- composestrtablefile
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tools:
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- gatk4:
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description:
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Genome Analysis Toolkit (GATK4). 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/articles/4405451249819-ComposeSTRTableFile
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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: ["Apache-2.0"]
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input:
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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- fasta_fai:
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type: file
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description: index of the FASTA reference file
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pattern: "*.fai"
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- dict:
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type: file
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description: Sequence dictionary of the FASTA reference file
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pattern: "*.dict"
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output:
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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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- str_table:
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type: file
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description: A zipped folder containing the STR table files
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pattern: "*.zip"
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authors:
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- "@nvnieuwk"
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@ -751,6 +751,10 @@ gatk4/combinegvcfs:
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- modules/gatk4/combinegvcfs/**
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- tests/modules/gatk4/combinegvcfs/**
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gatk4/composestrtablefile:
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- modules/gatk4/composestrtablefile/**
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- tests/modules/gatk4/composestrtablefile/**
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gatk4/createsequencedictionary:
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- modules/gatk4/createsequencedictionary/**
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- tests/modules/gatk4/createsequencedictionary/**
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16
tests/modules/gatk4/composestrtablefile/main.nf
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16
tests/modules/gatk4/composestrtablefile/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/gatk4/composestrtablefile/main.nf'
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workflow test_gatk4_composestrtablefile {
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fasta_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_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict )
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}
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5
tests/modules/gatk4/composestrtablefile/nextflow.config
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5
tests/modules/gatk4/composestrtablefile/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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7
tests/modules/gatk4/composestrtablefile/test.yml
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7
tests/modules/gatk4/composestrtablefile/test.yml
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- name: gatk4 composestrtablefile test_gatk4_composestrtablefile
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command: nextflow run ./tests/modules/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/composestrtablefile/nextflow.config
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tags:
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- gatk4/composestrtablefile
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- gatk4
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files:
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- path: output/gatk4/genome.zip
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