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https://github.com/MillironX/nf-core_modules.git
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new module: svtk/standardize (#2031)
* new module: svtk/standardize * linting * fixed tests
This commit is contained in:
nvnieuwk
GitHub
parent
3eb99152ce
commit
bf09fdf892
6 changed files with 217 additions and 4 deletions
45
modules/svtk/standardize/main.nf
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45
modules/svtk/standardize/main.nf
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@ -0,0 +1,45 @@
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process SVTK_STANDARDIZE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2':
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'quay.io/biocontainers/svtk:0.0.20190615--py37h73a75cf_2' }"
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input:
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tuple val(meta), path(vcf)
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path fasta_fai
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output:
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tuple val(meta), path("*.std.vcf.gz"), emit: standardized_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 arguments = args.args ?: ''
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def caller = args.caller ?: 'delly'
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def VERSION = '0.0.20190615' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def contigs = fasta_fai ? "--contigs ${fasta_fai}" : ""
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"""
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svtk standardize \\
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${arguments} \\
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${contigs} \\
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${vcf} \\
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${prefix}.std.vcf.gz \\
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${caller}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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svtk: ${VERSION}
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END_VERSIONS
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"""
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}
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61
modules/svtk/standardize/meta.yml
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61
modules/svtk/standardize/meta.yml
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@ -0,0 +1,61 @@
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name: "svtk_standardize"
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description: Convert SV calls to a standardized format.
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keywords:
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- svtk
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- structural variants
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- SV
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- vcf
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- standardization
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tools:
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- "svtk":
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description: "Utilities for consolidating, filtering, resolving, and annotating structural variants."
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homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
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documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
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tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
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doi: ""
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licence: "['MIT']"
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input:
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- args:
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type: map
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description: |
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Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes.
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```
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{
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[
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"args": "",
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"caller": "delly" // Should be either delly, lumpy, manta, wham or melt
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]
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}
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```
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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: A gzipped VCF file to be standardized
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pattern: "*.vcf.gz"
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- fasta_fai:
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type: file
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description: Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37)
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pattern: "*.fai"
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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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- standardized_vcf:
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type: file
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description: A gzipped version of the standardized VCF file
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pattern: "*.std.vcf.gz"
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authors:
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- "@nvnieuwk"
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@ -1538,14 +1538,14 @@ metabat2/metabat2:
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- modules/metabat2/metabat2/**
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- tests/modules/metabat2/metabat2/**
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metaphlan3/metaphlan3:
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- modules/metaphlan3/metaphlan3/**
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- tests/modules/metaphlan3/metaphlan3/**
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metaphlan3/mergemetaphlantables:
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- modules/metaphlan3/mergemetaphlantables/**
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- tests/modules/metaphlan3/mergemetaphlantables/**
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metaphlan3/metaphlan3:
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- modules/metaphlan3/metaphlan3/**
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- tests/modules/metaphlan3/metaphlan3/**
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methyldackel/extract:
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- modules/methyldackel/extract/**
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- tests/modules/methyldackel/extract/**
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@ -2263,6 +2263,10 @@ svdb/query:
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- modules/svdb/query/**
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- tests/modules/svdb/query/**
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svtk/standardize:
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- modules/svtk/standardize/**
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- tests/modules/svtk/standardize/**
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tabix/bgzip:
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- modules/tabix/bgzip/**
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- tests/modules/tabix/bgzip/**
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56
tests/modules/svtk/standardize/main.nf
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56
tests/modules/svtk/standardize/main.nf
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@ -0,0 +1,56 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SVTK_STANDARDIZE } from '../../../../modules/svtk/standardize/main.nf'
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include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
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workflow test_svtk_standardize {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
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]
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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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MANTA_GERMLINE(
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input,
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fasta,
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fasta_fai
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)
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SVTK_STANDARDIZE (
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MANTA_GERMLINE.out.diploid_sv_vcf,
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fasta_fai
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)
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}
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workflow test_svtk_standardize_no_contigs {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
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]
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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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MANTA_GERMLINE(
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input,
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fasta,
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fasta_fai
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)
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SVTK_STANDARDIZE (
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MANTA_GERMLINE.out.diploid_sv_vcf,
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[]
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)
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}
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12
tests/modules/svtk/standardize/nextflow.config
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12
tests/modules/svtk/standardize/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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withName: SVTK_STANDARDIZE {
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ext.args = [
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args : '',
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caller : 'manta'
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]
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}
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}
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35
tests/modules/svtk/standardize/test.yml
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35
tests/modules/svtk/standardize/test.yml
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- name: svtk standardize test_svtk_standardize
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command: nextflow run ./tests/modules/svtk/standardize -entry test_svtk_standardize -c ./tests/config/nextflow.config -c ./tests/modules/svtk/standardize/nextflow.config
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tags:
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- svtk
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- svtk/standardize
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files:
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- path: output/manta/test.candidate_small_indels.vcf.gz
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- path: output/manta/test.candidate_small_indels.vcf.gz.tbi
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md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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- path: output/manta/test.candidate_sv.vcf.gz
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- path: output/manta/test.candidate_sv.vcf.gz.tbi
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md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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- path: output/manta/test.diploid_sv.vcf.gz
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- path: output/manta/test.diploid_sv.vcf.gz.tbi
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md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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- path: output/svtk/test.std.vcf.gz
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md5sum: f7530f3bc7e6020e758cc996adc8ae35
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- name: svtk standardize test_svtk_standardize_no_contigs
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command: nextflow run ./tests/modules/svtk/standardize -entry test_svtk_standardize_no_contigs -c ./tests/config/nextflow.config -c ./tests/modules/svtk/standardize/nextflow.config
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tags:
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- svtk
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- svtk/standardize
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files:
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- path: output/manta/test.candidate_small_indels.vcf.gz
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- path: output/manta/test.candidate_small_indels.vcf.gz.tbi
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md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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- path: output/manta/test.candidate_sv.vcf.gz
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- path: output/manta/test.candidate_sv.vcf.gz.tbi
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md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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- path: output/manta/test.diploid_sv.vcf.gz
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- path: output/manta/test.diploid_sv.vcf.gz.tbi
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md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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- path: output/svtk/test.std.vcf.gz
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md5sum: ea67be7438a0fb72db8096e1bc1bb957
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