mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083)
* Added vcf_index to vcf tuple; output to vcf.gz format. * Fix: extra new line in meta.yml. * addressed review feedback * fix: editorconfig error * fix: gatk memory flag * fix: editorconfig error * fix: Indentation fix: Indentation * Fix: lint editorconfig error Removed one extra space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
This commit is contained in:
praveenraj2018
GitHub
parent
f052dc445c
commit
43a1c1c6d1
4 changed files with 65 additions and 23 deletions
|
|
@ -19,23 +19,29 @@ process GATK4_VARIANTFILTRATION {
|
|||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
tuple val(meta), path(vcf), path(vcf_tbi)
|
||||
path fasta
|
||||
path fai
|
||||
path dict
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.vcf"), emit: vcf
|
||||
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
||||
tuple val(meta), path("*.tbi") , emit: tbi
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.toGiga()
|
||||
}
|
||||
"""
|
||||
gatk VariantFiltration \\
|
||||
gatk --java-options "-Xmx${avail_mem}G" VariantFiltration \\
|
||||
-R $fasta \\
|
||||
-V $vcf \\
|
||||
-O ${prefix}.vcf \\
|
||||
-O ${prefix}.vcf.gz \\
|
||||
$options.args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
|
|||
|
|
@ -21,8 +21,12 @@ input:
|
|||
e.g. [ id:'test']
|
||||
- vcf:
|
||||
type: list
|
||||
description: Input VCF file
|
||||
pattern: "*.{vcf}"
|
||||
description: List of VCF(.gz) files
|
||||
pattern: "*.{vcf,vcf.gz}"
|
||||
- vcf_tbi:
|
||||
type: list
|
||||
description: List of VCF file indexes
|
||||
pattern: "*.{idx,tbi}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Fasta file of reference genome
|
||||
|
|
@ -38,8 +42,12 @@ input:
|
|||
output:
|
||||
- vcf:
|
||||
type: file
|
||||
description: filtered VCF file
|
||||
pattern: "*.filtered.{vcf}"
|
||||
description: Compressed VCF file
|
||||
pattern: "*.vcf.gz"
|
||||
- tbi:
|
||||
type: file
|
||||
description: Index of VCF file
|
||||
pattern: "*.vcf.gz.tbi"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
|
|
|
|||
|
|
@ -5,14 +5,32 @@ nextflow.enable.dsl = 2
|
|||
test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"', 'suffix': '.filtered']
|
||||
include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf' addParams( options: test_options )
|
||||
|
||||
workflow test_gatk4_variantfiltration {
|
||||
// Basic parameters with uncompressed VCF input
|
||||
workflow test_gatk4_variantfiltration_vcf_input {
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
|
||||
]
|
||||
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
|
||||
fai = [ file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
|
||||
genome_dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true) ]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_VARIANTFILTRATION ( input, fasta, fai, genome_dict )
|
||||
GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
|
||||
}
|
||||
|
||||
// Basic parameters with compressed VCF input
|
||||
workflow test_gatk4_variantfiltration_gz_input {
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -1,9 +1,19 @@
|
|||
- name: gatk4 variantfiltration test_gatk4_variantfiltration
|
||||
command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration -c tests/config/nextflow.config
|
||||
- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input
|
||||
command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4/variantfiltration
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.filtered.vcf
|
||||
contains:
|
||||
- "AC=2;AN=2;DP=1;DP4=0,0,1,0;MQ=60;MQ0F=0;SGB=-0.379885"
|
||||
- path: output/gatk4/test.filtered.vcf.gz
|
||||
contains: ['BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365']
|
||||
- path: output/gatk4/test.filtered.vcf.gz.tbi
|
||||
|
||||
- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input
|
||||
command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4/variantfiltration
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.filtered.vcf.gz
|
||||
contains: ['BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365']
|
||||
- path: output/gatk4/test.filtered.vcf.gz.tbi
|
||||
|
|
|
|||
Loading…
Reference in a new issue