millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

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

Browse source 
* 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
Show stats Download patch file Download diff file Expand all files Collapse all files

6
modules/plink2/vcf/main.nf
View file

@ -13,7 +13,7 @@ process PLINK2_VCF {
output: output:
tuple val(meta), path("*.pgen") , emit: pgen tuple val(meta), path("*.pgen") , emit: pgen
tuple val(meta), path("*.psam") , emit: psam tuple val(meta), path("*.psam") , emit: psam
tuple val(meta), path("*.pvar"), emit: pvar tuple val(meta), path("*.pvar.zst"), emit: pvar
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -22,10 +22,14 @@ process PLINK2_VCF {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def mem_mb = task.memory.toMega()
""" """
plink2 \\ plink2 \\
--threads $task.cpus \\
--memory $mem_mb \\
$args \\ $args \\
--vcf $vcf \\ --vcf $vcf \\
--make-pgen vzs \\
--out ${prefix} --out ${prefix}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

2
modules/plink2/vcf/meta.yml
View file

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

10
tests/modules/plink2/vcf/test.yml
View file

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