Whishlist

[kloetzl]

Here is an assorted list of tools for which completions might be of interest to some users.

• [ ] annovar
• [ ] bamstats
• [ ] bcftools
• [ ] beagle
• [ ] BigWig
• [ ] bismark
• [ ] callisto
• [ ] chimira
• [ ] cufflinks
• [ ] cutadapt
• [ ] # DEseq2 - not a command line tool
• [x] Diamond — Done by @cgjosephlee in #9
• [ ] edgeR
• [ ] elprep
• [ ] exomedepth
• [ ] impute
• [ ] kraken
• [ ] micca
• [ ] muscan
• [ ] nextgenmap
• [ ] Picard
• [ ] pindel
• [ ] qualimap
• [ ] quiime2
• [ ] sambamba
• [ ] scalpel
• [ ] sleuth
• [ ] snpeff
• [ ] star
• [ ] sylamer
• [ ] tandemrepeatsfinder
• [ ] tophat2
• [ ] trimgalore
• [ ] varscan2
• [ ] vntrseek
• [ ] zoom

[cgjosephlee]

Hi @kloetzl, thank you for awesome plugin. I'm new to zsh community, and I'm trying to work on diamond autocomplete script. Since many subcommands in diamond share same options (e.g. blastx, blastp), are there any clever way to share options between subcommands instead of duplicating them?

[kloetzl]

As long as all your subcommands are handled within the same completion script you could declare a global variable containing the shared options and add those to the individual options. The exact syntax may differ from case to case.