mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-21 10:48:18 +00:00
add stub and the option to compress output for vep (#2111)
* add stub * create tab and json files * add option to get compressed outputs
This commit is contained in:
Ramprasad Neethiraj
GitHub
parent
e9bc33485e
commit
3d7ce93630
4 changed files with 85 additions and 6 deletions
|
|
@ -17,11 +17,14 @@ process ENSEMBLVEP {
|
|||
path extra_files
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.ann.vcf") , optional:true, emit: vcf
|
||||
tuple val(meta), path("*.ann.tab") , optional:true, emit: tab
|
||||
tuple val(meta), path("*.ann.json") , optional:true, emit: json
|
||||
path "*.summary.html" , emit: report
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path("*.ann.vcf") , optional:true, emit: vcf
|
||||
tuple val(meta), path("*.ann.tab") , optional:true, emit: tab
|
||||
tuple val(meta), path("*.ann.json") , optional:true, emit: json
|
||||
tuple val(meta), path("*.ann.vcf.gz") , optional:true, emit: vcf_gz
|
||||
tuple val(meta), path("*.ann.tab.gz") , optional:true, emit: tab_gz
|
||||
tuple val(meta), path("*.ann.json.gz") , optional:true, emit: json_gz
|
||||
path "*.summary.html" , emit: report
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
|
@ -29,6 +32,7 @@ process ENSEMBLVEP {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf'
|
||||
def compress_out = args.contains("--compress_output") ? '.gz' : ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
|
||||
def reference = fasta ? "--fasta $fasta" : ""
|
||||
|
|
@ -36,7 +40,7 @@ process ENSEMBLVEP {
|
|||
"""
|
||||
vep \\
|
||||
-i $vcf \\
|
||||
-o ${prefix}.ann.${file_extension} \\
|
||||
-o ${prefix}.ann.${file_extension}${compress_out} \\
|
||||
$args \\
|
||||
$reference \\
|
||||
--assembly $genome \\
|
||||
|
|
@ -48,6 +52,23 @@ process ENSEMBLVEP {
|
|||
--stats_file ${prefix}.summary.html \\
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
stub:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
touch ${prefix}.ann.vcf
|
||||
touch ${prefix}.ann.tab
|
||||
touch ${prefix}.ann.json
|
||||
touch ${prefix}.ann.vcf.gz
|
||||
touch ${prefix}.ann.tab.gz
|
||||
touch ${prefix}.ann.json.gz
|
||||
touch ${prefix}.summary.html
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
|
||||
|
|
|
|||
|
|
@ -7,6 +7,8 @@ include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
|
|||
include { ENSEMBLVEP as ENSEMBLVEP_JSON } from '../../../modules/ensemblvep/main.nf'
|
||||
include { ENSEMBLVEP as ENSEMBLVEP_TAB } from '../../../modules/ensemblvep/main.nf'
|
||||
include { ENSEMBLVEP as ENSEMBLVEP_VCF } from '../../../modules/ensemblvep/main.nf'
|
||||
include { ENSEMBLVEP as ENSEMBLVEP_VCF_BGZIP } from '../../../modules/ensemblvep/main.nf'
|
||||
include { ENSEMBLVEP as ENSEMBLVEP_VCF_GZIP } from '../../../modules/ensemblvep/main.nf'
|
||||
|
||||
workflow test_ensemblvep_fasta_json {
|
||||
input = [
|
||||
|
|
@ -41,6 +43,28 @@ workflow test_ensemblvep_fasta_vcf {
|
|||
ENSEMBLVEP_VCF ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
|
||||
}
|
||||
|
||||
workflow test_ensemblvep_fasta_vcf_bgzip {
|
||||
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)
|
||||
|
||||
ENSEMBLVEP_VCF_BGZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
|
||||
}
|
||||
|
||||
workflow test_ensemblvep_fasta_vcf_gzip {
|
||||
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)
|
||||
|
||||
ENSEMBLVEP_VCF_GZIP ( input, "WBcel235", "caenorhabditis_elegans", "106", [], fasta, [] )
|
||||
}
|
||||
|
||||
workflow test_ensemblvep_fasta {
|
||||
input = [
|
||||
[ id:'test' ], // meta map
|
||||
|
|
|
|||
|
|
@ -20,4 +20,14 @@ process {
|
|||
container = 'nfcore/vep:106.1.WBcel235'
|
||||
ext.args = '--vcf'
|
||||
}
|
||||
|
||||
withName: ENSEMBLVEP_VCF_BGZIP {
|
||||
container = 'nfcore/vep:106.1.WBcel235'
|
||||
ext.args = '--vcf --compress_output bgzip'
|
||||
}
|
||||
|
||||
withName: ENSEMBLVEP_VCF_GZIP {
|
||||
container = 'nfcore/vep:106.1.WBcel235'
|
||||
ext.args = '--vcf --compress_output gzip'
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -22,6 +22,22 @@
|
|||
- path: output/ensemblvep/test.ann.vcf
|
||||
- path: output/ensemblvep/test.summary.html
|
||||
|
||||
- name: ensemblvep test_ensemblvep_fasta_vcf_bgzip
|
||||
command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
|
||||
tags:
|
||||
- ensemblvep
|
||||
files:
|
||||
- path: output/ensemblvep/test.ann.vcf.gz
|
||||
- path: output/ensemblvep/test.summary.html
|
||||
|
||||
- name: ensemblvep test_ensemblvep_fasta_vcf_gzip
|
||||
command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf_gzip -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
|
||||
tags:
|
||||
- ensemblvep
|
||||
files:
|
||||
- path: output/ensemblvep/test.ann.vcf.gz
|
||||
- path: output/ensemblvep/test.summary.html
|
||||
|
||||
- name: ensemblvep test_ensemblvep_fasta
|
||||
command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
|
||||
tags:
|
||||
|
|
@ -37,3 +53,11 @@
|
|||
files:
|
||||
- path: output/ensemblvep/test.ann.vcf
|
||||
- path: output/ensemblvep/test.summary.html
|
||||
|
||||
- name: ensemblvep test_ensemblvep_fasta_vcf_stub
|
||||
command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep_fasta_vcf -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config -stub
|
||||
tags:
|
||||
- ensemblvep
|
||||
files:
|
||||
- path: output/ensemblvep/test.ann.vcf
|
||||
- path: output/ensemblvep/test.summary.html
|
||||
|
|
|
|||
Loading…
Reference in a new issue