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Improvement: make --tools case insensitive #1187

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adamrtalbot opened this issue Aug 18, 2023 · 1 comment · May be fixed by #1188
Open

Improvement: make --tools case insensitive #1187

adamrtalbot opened this issue Aug 18, 2023 · 1 comment · May be fixed by #1188
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enhancement New feature or request

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@adamrtalbot
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Description of feature

--tools can be tricky to understand. A little change we could add would make it case insensitive, meaning if someone wrote --tools Mutect2 it would still work. This could be done by changing every:

params.skip_tools.split(',').contains('mutect2')

to:

params.skip_tools.split(',').toLowerCase().contains('mutect2')

Given how many times this pattern is used, we could also add it to a function.
@adamrtalbot adamrtalbot added the enhancement New feature or request label Aug 18, 2023
adamrtalbot added a commit to adamrtalbot/sarek that referenced this issue Aug 18, 2023
@adamrtalbot
Added: --tools now case insensitive
3b70073 
Fixes nf-core#1187
@adamrtalbot adamrtalbot linked a pull request Aug 18, 2023 that will close this issue
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@asp8200
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asp8200 commented Aug 19, 2023 •
edited

@adamrtalbot : The change should be made for both --tools and --skip_tools, right? (EDIT: I now see you already did the PR for both parameters :-) )

How about making the change just one place centrally? Something like

params.skip_tools = params.skip_tools.toLowerCase()

in sarek.nf?

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[WIP] --tools is now case insensitive adamrtalbot/sarek
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@adamrtalbot @asp8200