Update plink2/vcf to output zstandard compressed data automatically (#1258)

* update plink2/vcf to output zstandard compressed data automatically

* update meta

* set plink CPU and memory usage

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
This commit is contained in:
Benjamin Wingfield 2022-03-02 00:43:28 +00:00 committed by GitHub
parent 4ab098733a
commit 8e5eaf1fa4
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
3 changed files with 15 additions and 9 deletions

View file

@ -11,10 +11,10 @@ process PLINK2_VCF {
tuple val(meta), path(vcf)
output:
tuple val(meta), path("*.pgen"), emit: pgen
tuple val(meta), path("*.psam"), emit: psam
tuple val(meta), path("*.pvar"), emit: pvar
path "versions.yml" , emit: versions
tuple val(meta), path("*.pgen") , emit: pgen
tuple val(meta), path("*.psam") , emit: psam
tuple val(meta), path("*.pvar.zst"), emit: pvar
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -22,10 +22,14 @@ process PLINK2_VCF {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def mem_mb = task.memory.toMega()
"""
plink2 \\
--threads $task.cpus \\
--memory $mem_mb \\
$args \\
--vcf $vcf \\
--make-pgen vzs \\
--out ${prefix}
cat <<-END_VERSIONS > versions.yml

View file

@ -46,7 +46,7 @@ output:
- pvar:
type: file
description: PLINK 2 variant information file
pattern: "*.{psam}"
pattern: "*.{pvar.zst}"
authors:
- "@nebfield"

View file

@ -1,12 +1,14 @@
- name: plink2 vcf test_plink2_vcf
command: nextflow run ./tests/modules/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink2/vcf/nextflow.config
command: nextflow run tests/modules/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config
tags:
- plink2/vcf
- plink2
- plink2/vcf
files:
- path: output/plink2/test.pgen
md5sum: d66d3cd4a6c9cca1a4073d7f4b277041
- path: output/plink2/test.psam
md5sum: dc3b77d7753a7bed41734323e3549b10
- path: output/plink2/test.pvar
md5sum: d61e53f847a6335138b584216b4e45d0
- path: output/plink2/test.pvar.zst
md5sum: b53cccb83e024a39789af5eab8de1c28
- path: output/plink2/versions.yml
md5sum: 82ada74bc81473b7cba377f696acf54c