[FEATURE] Optional output from VEP in vcf-, json- or tab-format #1774
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* 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 <[email protected]> Co-authored-by: nvnieuwk <[email protected]>
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Is your feature request related to a problem? Please describe
As part of the Sarek-project, we would like the VEP-module
ENSEMBLVEP(modules/ensemblvep/main.nf) could be configured to output either a vcf-file, a json-file or a tab-file, c.f. nf-core/sarek#575Describe the solution you'd like
The output-file-format is controlled through
task.ext.argswhile the output-file-extension is set bytask.ext.args2. This approach was developed with @maxulysse and @FriederikeHanssen, here: nf-core/sarek#582Describe alternatives you've considered
No response
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