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Add subcommand level --verbose for nf-core modules tests #2554

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jfy133 opened this issue Dec 5, 2023 · 4 comments
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Add subcommand level --verbose for nf-core modules tests #2554

jfy133 opened this issue Dec 5, 2023 · 4 comments
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command line tools Anything to do with the cli interfaces good-first-issue

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@jfy133
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jfy133 commented Dec 5, 2023

Description of feature

Currently you can get verbose module (and presumably subworkflow) nf-test verbose/debugging logs by asking for --verbose at the tools level.

I find this unintuitive as if I'm looking for nf-test logs, I wouldn't ask at the nf-core level as I'm not interested in nf-core logs at the same time.

e.g. I want to find out why my nf-test failed

nf-core --verbose modules test <module>

doesn't make sense to me, but rather

nf-core modules test --verbose <module>
## OR
nf-core modules test <module> --verbose

Does, as it 'feels' like I'm assking the --verbose log for the test itself. However this gives an error of an unrecognised option

More details here: https://nfcore.slack.com/archives/CE5LG7WMB/p1701779689455179

That said the 'mixed' --verbose isn't so messy. As a fast work around could just alias a modules test level verbose to the general nf-core one.

@mashehu mashehu added command line tools Anything to do with the cli interfaces good-first-issue and removed enhancement labels Jan 9, 2024
@Femi-lawal
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@jfy133 @mashehu Hi, please can I work on this?

@mashehu
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mashehu commented Feb 5, 2024

Sure, give it a try! You can tag me or @mirpedrol here or on the nf-core slack if you need some help.

@LaurenceKuhl LaurenceKuhl self-assigned this Aug 15, 2024
@LaurenceKuhl
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Hi @Femi-lawal, I'd have a look if you haven't yet?

@LaurenceKuhl
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Hi, this is now done in #3120 so closing this issue :)

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