Merge pull request #1652 from lmtani/haplocheck

Add Haplocheck
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Taniguti 2022-06-11 08:50:24 -03:00 committed by GitHub
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process HAPLOCHECK {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::haplocheck=1.3.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0':
'quay.io/biocontainers/haplocheck:1.3.3--h4a94de4_0' }"
input:
tuple val(meta), path(vcf)
output:
tuple val(meta), path("*.txt") , emit: txt
tuple val(meta), path("*.html"), emit: html
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
haplocheck --raw --out $prefix $vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.raw.txt
touch ${prefix}.html
cat <<-END_VERSIONS > versions.yml
"${task.process}":
haplocheck: \$(echo \$(haplocheck --version 2>&1) | cut -f 2 -d " " )
END_VERSIONS
"""
}

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name: "haplocheck"
description: |
Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing
the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides
users a graphical report to investigate the contamination further. Internally, it uses the
Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.
keywords:
- mitochondrial
- mtDNA
- contamination
tools:
- "haplocheck":
description: "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content."
homepage: "https://github.com/genepi/haplocheck"
documentation: "https://github.com/genepi/haplocheck"
tool_dev_url: "https://github.com/genepi/haplocheck"
doi: 10.1101/gr.256545.119
licence: "['MIT']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF file
pattern: "*.{vcf.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- txt:
type: file
description: Raw report in txt format
pattern: "*.{txt}"
- html:
type: file
description: Haplocheck HTML report
pattern: "*.{html}"
authors:
- "@lmtani"

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@ -967,6 +967,10 @@ hamronization/summarize:
- modules/hamronization/summarize/**
- tests/modules/hamronization/summarize/**
haplocheck:
- modules/haplocheck/**
- tests/modules/haplocheck/**
happy/happy:
- modules/happy/happy/**
- tests/modules/happy/happy/**

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@ -329,6 +329,8 @@ params {
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_mito_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz"
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
test_flowcell = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HAPLOCHECK } from '../../../modules/haplocheck/main.nf'
workflow test_haplocheck {
input = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_mito_vcf'], checkIfExists: true)
]
HAPLOCHECK ( input )
}

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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- name: haplocheck test_haplocheck
command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config
tags:
- haplocheck
files:
- path: output/haplocheck/test.html
md5sum: 59d69052c86edff0301816956eaf4d5f
- path: output/haplocheck/test.raw.txt
md5sum: 69f4e5b28a59b97fc19eb8e8b650d9d5
- path: output/haplocheck/versions.yml
md5sum: 94e2fa3ceb3946487319f92cea08c942
- name: haplocheck test_haplocheck using stubs
command: nextflow run ./tests/modules/haplocheck -entry test_haplocheck -c ./tests/config/nextflow.config -c ./tests/modules/haplocheck/nextflow.config -stub-run
tags:
- haplocheck
files:
- path: output/haplocheck/test.html
- path: output/haplocheck/test.raw.txt
- path: output/haplocheck/versions.yml