8000 new module: custom/awk_fai_to_bed · Issue #5132 · nf-core/modules · GitHub
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new module: custom/awk_fai_to_bed #5132

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maxulysse opened this issue Mar 15, 2024 · 9 comments
Closed
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new module: custom/awk_fai_to_bed #5132

maxulysse opened this issue Mar 15, 2024 · 9 comments
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@maxulysse
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maxulysse commented Mar 15, 2024 •
edited by vcepeda
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Is there an existing module for this?

  • I have searched for the existing module

Is there an open PR for this?

  • I have searched for existing PRs

Is there an open issue for this?

  • I have searched for existing issues

Are you going to work on this?

  • If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module
@maxulysse maxulysse added the new module Adding a new module label Mar 15, 2024
@maxulysse
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cf
https://github.com/nf-core/sarek/blob/master/modules/local/build_intervals/main.nf
https://github.com/nf-core/raredisease/blob/master/modules/local/create_bed_from_fai.nf

@asp8200 asp8200 self-assigned this Mar 15, 2024
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asp8200 commented Mar 15, 2024

@maxulysse : Maybe I can do this one? It seems the main thing is to write some nf-test tests for the "new" module, right?

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asp8200 commented Mar 17, 2024

@maxulysse : Concerning the proposed name of the new module - the nf-core tool doesn't like underscores in the name of modules. How about we go with custom/faitobed?

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asp8200 commented Mar 17, 2024

Made this draft, but couldn't the nf-core module gawk be used instead?

@asp8200 asp8200 mentioned this issue Mar 18, 2024
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@asp8200 asp8200 moved this to In progress in Hackathon: May 2024 Mar 18, 2024
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Since this is a stand-alone process just for awk, it looks to me like a very good use case for the gawk module. (If it were a line in some other process, a module would be overkill, but for this it seems like a perfect fit.)

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asp8200 commented Mar 18, 2024

@maxulysse : How about I make a PR to Sarek where I replace local/buid_intervals with nf-core/gawk?

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Yeah, let's see if you can make it work

@asp8200 asp8200 mentioned this issue Mar 18, 2024
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asp8200 commented Mar 18, 2024

@maxulysse @tdanhorn @ramprasadn : What do you think about this?

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@maxulysse @tdanhorn @ramprasadn : What do you think about this?

PURE GENIUS

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