https://nf-co.re logo
Join Slack
Powered by
Before I make an issue, I want to check if there i...
# tools
j
Before I make an issue, I want to check if there is already an issue on this but I don't know how to search for this: Is there a plan to support ways of linting/testing all subcommand modules by specifyhing the parent tool name? e.g. 
bwa
actually has 
bwa/aln
`bwa/mem`bwa/index` I want to lint or update snapshots for all, I instinctively want to be able to go:
Copy code
nf-core modules lint bwa
## OR
nf-core modules lint bwa/*
but this doesn't work. Is this something on a roadmap/issue already, or should I make one? @moritz and @Maxime Garcia both said they would like this too :)
m
I would like this too! Would also be handy to test all subtools
j
@Phil Ewels would that make your PR in the other channel easier too?
m
The help text actually suggests that it is/was possible.
Copy code
Usage: nf-core modules lint [OPTIONS] <tool> or <tool/subtool>
m
It's there already
j
IT doesn't work for me
Copy code
$ nf-core modules lint bwa


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.3.2 - <https://nf-co.re>


^[[AERROR    Could not find the specified module: 'bwa'
Copy code
$ nf-core modules lint bwa/


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.3.2 - <https://nf-co.re>


ERROR    Could not find the specified module: 'bwa/'
@mashehu does that mean I should make a bug report issue?
m
Try the dev version
I am pretty sure I merged that before I left, but could still be out there (try without the slash)
And might just be for update maybe?
It is for now only for bump-version
👍 1
j
Ahhh ok that's the one I didn't try, should I make an issue for lint and test too?
m
Yes, please
j
Open in Slack
PreviousNext
Powered by