Add a parameter corresponding to -canonList <file> option of snpEff ann
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Description
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).
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@maxulysse Thank you!
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Research direction
Start at the SNPEFF_SNPEFF process and inspect how its parameters are defined and passed to the snpEff ann command. Add the canonList path parameter and verify that a supplied tab-separated gene/transcript file is passed through when the process runs.
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Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100