implement plink2/score module (#1259)

* implement plink2/score module

* fix test yml

* fix typo :(

* set cpu

* set mem

* fix input process input block

* fix tests

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
This commit is contained in:
Benjamin Wingfield 2022-03-07 18:02:40 +00:00 committed by GitHub
parent 251015c8ba
commit de0d57a562
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7 changed files with 156 additions and 1 deletions

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@ -0,0 +1,39 @@
process PLINK2_SCORE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
input:
tuple val(meta), path(pgen), path(psam), path(pvar)
path(scorefile)
output:
tuple val(meta), path("*.sscore"), emit: score
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}"
def mem_mb = task.memory.toMega() // plink is greedy
"""
plink2 \\
--threads $task.cpus \\
--memory $mem_mb \\
--pfile ${pgen.baseName} vzs \\
--score ${scorefile} \\
$args \\
--out ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
END_VERSIONS
"""
}

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@ -0,0 +1,56 @@
name: plink2_score
description: Apply a scoring system to each sample in a plink 2 fileset
keywords:
- plink2
- score
tools:
- plink2:
description: |
Whole genome association analysis toolset, designed to perform a range
of basic, large-scale analyses in a computationally efficient manner
homepage: http://www.cog-genomics.org/plink/2.0/
documentation: http://www.cog-genomics.org/plink/2.0/general_usage
tool_dev_url: None
doi: "10.1186/s13742-015-0047-8"
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- pgen:
type: file
description: PLINK 2 binary genotype table
pattern: "*.{pgen}"
- psam:
type: file
description: PLINK 2 sample information file
pattern: "*.{psam}"
- pvar:
type: file
description: PLINK 2 variant information file
pattern: "*.{pvar}"
- scorefile:
type: file
description: A text file containing variant identifiers and weights
pattern: "*.{scores,txt,scorefile}"
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"
- score:
type: file
description: A text file containing sample scores, in plink 2 .sscore format
pattern: "*.{sscore}"
authors:
- "@nebfield"

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@ -1273,6 +1273,10 @@ plink2/extract:
- modules/plink2/extract/**
- tests/modules/plink2/extract/**
plink2/score:
- modules/plink2/score/**
- tests/modules/plink2/score/**
plink2/vcf:
- modules/plink2/vcf/**
- tests/modules/plink2/vcf/**

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@ -119,7 +119,7 @@ params {
genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
@ -138,6 +138,7 @@ params {
mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
syntheticvcf_short_score = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
gnomad_r2_1_1_sv_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
hapmap_3_3_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"

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@ -0,0 +1,24 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
include { PLINK2_SCORE } from '../../../../modules/plink2/score/main.nf'
workflow test_plink2_score {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
]
PLINK2_VCF ( input )
scorefile = file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_score'], checkIfExists: true)
PLINK2_VCF.out.pgen
.concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar)
.groupTuple()
.map { it.flatten() }
.set { ch_target_genome }
PLINK2_SCORE ( ch_target_genome, scorefile )
}

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@ -0,0 +1,15 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
// relabel input variants to a common scheme chr:pos:alt:ref
withName: PLINK2_VCF {
ext.args = '--set-missing-var-ids @:#:\\$1:\\$2'
}
// scoring really needs an adjustment for small test dataset (n > 50
// normally)
withName: PLINK2_SCORE {
ext.args = 'no-mean-imputation'
}
}

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@ -0,0 +1,16 @@
- name: plink2 score test_plink2_score
command: nextflow run tests/modules/plink2/score -entry test_plink2_score -c tests/config/nextflow.config
tags:
- plink2
- plink2/score
files:
- path: output/plink2/test.pgen
md5sum: fac12ca9041d6950f6b7d60ac2120721
- path: output/plink2/test.psam
md5sum: e6c714488754cb8448c3dfda08c4c0ea
- path: output/plink2/test.pvar.zst
md5sum: 98d59e9779a8b62d5032cd98b642a63b
- path: output/plink2/test.sscore
md5sum: 97bde840f69febd65f2c00e9243126e9
- path: output/plink2/versions.yml
md5sum: 71499ab14e1583c88ced3a7a4f05bfa7