mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
added dragstr model to haplotypecaller
This commit is contained in:
Nicolas Vannieuwkerke
parent
5447395975
commit
e53d091a6d
5 changed files with 42 additions and 8 deletions
|
|
@ -8,7 +8,7 @@ process GATK4_HAPLOTYPECALLER {
|
|||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
|
||||
path fasta
|
||||
path fai
|
||||
path dict
|
||||
|
|
@ -28,6 +28,7 @@ process GATK4_HAPLOTYPECALLER {
|
|||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
|
||||
def interval_command = intervals ? "--intervals $intervals" : ""
|
||||
def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : ""
|
||||
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
|
|
@ -42,6 +43,7 @@ process GATK4_HAPLOTYPECALLER {
|
|||
--reference $fasta \\
|
||||
$dbsnp_command \\
|
||||
$interval_command \\
|
||||
$dragstr_command \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
|
|
|
|||
|
|
@ -32,6 +32,10 @@ input:
|
|||
- intervals:
|
||||
type: file
|
||||
description: Bed file with the genomic regions included in the library (optional)
|
||||
- dragstr_model:
|
||||
type: file
|
||||
description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
|
||||
pattern: "*.txt"
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference fasta file
|
||||
|
|
|
|||
|
|
@ -266,6 +266,8 @@ params {
|
|||
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
|
||||
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
||||
|
||||
test_paired_end_sorted_dragstrmodel = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt"
|
||||
|
||||
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
||||
test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
|
||||
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ workflow test_gatk4_haplotypecaller {
|
|||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
||||
[],
|
||||
[]
|
||||
]
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
@ -21,6 +22,7 @@ workflow test_gatk4_haplotypecaller_cram {
|
|||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
[],
|
||||
[]
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
@ -34,7 +36,8 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
|
|||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
@ -45,3 +48,20 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
|
|||
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
|
||||
}
|
||||
|
||||
workflow test_gatk4_haplotypecaller_dragstr_model {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
[],
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true)
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||||
sites = []
|
||||
sites_tbi = []
|
||||
|
||||
GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,7 +6,6 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
|
||||
command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
|
||||
|
|
@ -16,7 +15,6 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
|
||||
command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
|
||||
|
|
@ -26,4 +24,12 @@
|
|||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
|
||||
command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
|
||||
tags:
|
||||
- gatk4/haplotypecaller
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.vcf.gz
|
||||
- path: output/gatk4/test.vcf.gz.tbi
|
||||
|
|
|
|||
Loading…
Reference in a new issue