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nf-core / modules

Repository to host tool-specific module files for the Nextflow DSL2 community!
https://nf-co.re/modules
MIT License
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Add a parameter corresponding to -canonList <file> option of snpEff ann #3822

Open YeHW opened 10 months ago

YeHW commented 10 months ago

Description of feature

snpEff ann command has an option: -canonList <file>, that can take in a tab-separated file containing gene and transcript.

-canonList : Only use canonical transcripts, replace some transcripts using the `gene_id transcript_id` entries in \<file>.

Propose to add a parameter (e.g. snpeff_canon_list), whose value should be a string indicating the path of the canonList file - Allowing users to supply custom canonList file to be used with snpEff ann command (SNPEFF_SNPEFF process).

Discussion on slack. @maxulysse Thank you!

maxulysse commented 10 months ago

Do you have any example of what this file could looks like?

maxulysse commented 10 months ago

Hi @YeHW I transferred the issue in https://github.com/nf-core/modules

YeHW commented 10 months ago

Do you have any example of what this file could looks like?

Yeah, it should be a tab-delimited file with two columns, corresponding to gene and transcript. canonList.txt

YeHW commented 10 months ago

Hi @YeHW I transferred the issue in https://github.com/nf-core/modules

Sure, thanks!