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Fix param arg_amrfinderplus_name #369

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Fix param arg_amrfinderplus_name #369

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m3hdad
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@m3hdad m3hdad commented May 2, 2024

Module configuration could not read meta.id if --arg_amrfinderplus_name is set true.
ext.args at module.conf needs to be wrapped in curly brackets and double quotation around --name ${meta.id}.

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@jfy133 jfy133 requested review from jasmezz and Darcy220606 May 2, 2024 13:54
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github-actions bot commented May 2, 2024

nf-core lint overall result: Passed ✅

Posted for pipeline commit eac0e87

+| ✅ 236 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-02 13:57:28

jasmezz
jasmezz requested changes May 2, 2024
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Looks basically good. I tested the --arg_amrfinderplus_name parameter locally. I am just confused, that your PR from master branch on your fork to dev changes just 1 file (many others should have changed between master and dev). I would have assumend a PR from a new dev branch would be the correct way. But I don't mind if it works as is 🤷
Just please add this line to the CHANGELOG.md file in the "fixed" section:

[#369](https://github.com/nf-core/funcscan/pull/369) Fixed AMRFinderPlus parameter `arg_amrfinderplus_name`. (by @m3hdad)

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m3hdad commented May 2, 2024

Looks basically good. I tested the --arg_amrfinderplus_name parameter locally. I am just confused, that your PR from master branch on your fork to dev changes just 1 file (many others should have changed between master and dev). I would have assumend a PR from a new dev branch would be the correct way. But I don't mind if it works as is 🤷 Just please add this line to the CHANGELOG.md file in the "fixed" section:

[#369](https://github.com/nf-core/funcscan/pull/369) Fixed AMRFinderPlus parameter `arg_amrfinderplus_name`. (by @m3hdad)

Uuh I see that now! CHANGELOG.md don't match then for dev branch. You should be able to edit change log on dev directly, if not, then we have to kill this one and do a new PR. Sorry my bad!

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jasmezz commented May 3, 2024

Alright, we don't commit to dev branch, only pull requests go in ;) So either you create a new PR or I revive my closed one from yesterday.

@jasmezz jasmezz closed this May 3, 2024
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@jasmezz jasmezz jasmezz requested changes

@Darcy220606 Darcy220606 Awaiting requested review from Darcy220606

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