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Add how to supply ext args with params #2832

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merged 10 commits into from
Nov 19, 2024

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mahesh-panchal
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@mahesh-panchal mahesh-panchal commented Oct 30, 2024

Add description to website how to use params to supply nextflow config in modules nf-core/modules#6788

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jfy133 commented Oct 31, 2024

And should add mention of this in teh modules specs

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@JoseEspinosa JoseEspinosa left a comment

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LGTM!

I just add a small suggestion

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I forgot to finish a review, sorry @mahesh-panchal

}
```

```groovy title="nextflow.config"
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Should we say nothing else should go in this file?

Also I think there is a broken code block somewhere earlier in this poage, the syntax highlight is off here...

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I added something, although I don't think it's really necessary.

The syntax highlighting looked OK to me. Can you describe what's off?

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I haven't checked the deploy preview admittedly, but in the github reviewing context, the normal text that should be white is blue like it thinks it's code:

image

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Ah, OK. I think I found it around line 184. I'll see if it fixes it.

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There's something I don't understand on Line 193 now that changes formatting.

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@mashehu Any idea why the highlighting goes funny on Line 196?

@mahesh-panchal mahesh-panchal force-pushed the nftest_config_advice branch 2 times, most recently from 3b0faf8 to bae7d2c Compare November 5, 2024 12:42
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Awesome idea. I think it'll help cut down on the "where did that come from?" feeling of the tests.

More importantly do we have an issue to create linting around this?

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mashehu commented Nov 14, 2024

More importantly do we have an issue to create linting around this?

what exactly should we lint for?

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More importantly do we have an issue to create linting around this?

what exactly should we lint for?

A single nextflow.config file in tests, and that it contains the string ext.args = params., and not ext.args = [{'"]

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jfy133 commented Nov 19, 2024

@mahesh-panchal you can merge in now, unless you want to wait for the linting test

@mahesh-panchal mahesh-panchal merged commit 9ea0489 into nf-core:main Nov 19, 2024
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@mahesh-panchal mahesh-panchal deleted the nftest_config_advice branch November 19, 2024 10:49
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5 participants