mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
30f72e2482
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774 * Trying to fix tests * Still trying to fix tests * Fetching the vep-output-file-extension from the args. * Update meta.yml * WIP: Adding tests for vep-output json and tab * updated the test.yml Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
23 lines
541 B
Text
23 lines
541 B
Text
process {
|
|
|
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
|
|
|
withName: ENSEMBLVEP {
|
|
container = 'nfcore/vep:104.3.WBcel235'
|
|
}
|
|
|
|
withName: ENSEMBLVEP_JSON {
|
|
container = 'nfcore/vep:104.3.WBcel235'
|
|
ext.args = '--json'
|
|
}
|
|
|
|
withName: ENSEMBLVEP_TAB {
|
|
container = 'nfcore/vep:104.3.WBcel235'
|
|
ext.args = '--tab'
|
|
}
|
|
|
|
withName: ENSEMBLVEP_VCF {
|
|
container = 'nfcore/vep:104.3.WBcel235'
|
|
ext.args = '--vcf'
|
|
}
|
|
}
|