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JSON Help + Lib Functions adding#680

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jfy133 merged 26 commits intodevfrom
add-fancy-help-json-for-james
Mar 12, 2021
Merged

JSON Help + Lib Functions adding#680
jfy133 merged 26 commits intodevfrom
add-fancy-help-json-for-james

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@apeltzer apeltzer commented Feb 5, 2021

As on the tin this adds:

  • Automated help generation from JSON
  • Summary generation from JSON
  • Some extra functions (e.g. awsbatch checks, hostname checks) are callable from the external lib now

We could have the same as in rnaseq:

  • check conda channels for correctness (!)
  • ...

@apeltzer apeltzer requested a review from jfy133 February 5, 2021 19:54
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apeltzer commented Feb 5, 2021

Fixes #676

@apeltzer apeltzer self-assigned this Feb 5, 2021
@apeltzer apeltzer added the WIP Work in progress label Feb 5, 2021
@apeltzer apeltzer marked this pull request as draft February 5, 2021 20:02
@apeltzer apeltzer marked this pull request as ready for review February 8, 2021 09:40
@apeltzer apeltzer removed the WIP Work in progress label Feb 8, 2021
@apeltzer apeltzer mentioned this pull request Feb 8, 2021
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apeltzer commented Feb 15, 2021 •
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Ok, just switched over to the newest lib adding in functionality from here nf-core/tools#852

Note, that I have NOT changed how we do the help + summary, as the newest nf-core template will NOT contain that most likely for now. I've intentionally kept that in the Schema.groovy file and the main validation stuff in the NfcoreSchema.groovy part that will be kept up2date via nf-core sync later. This will make our lifes easier hopefully ;-)

I also dropped the libraries to the one provided by @KevinMenden that shrinks it to a single library we ship with pipelines soon.

Schema.groovy:

  • help
  • summary
  • multiqc summary stuff

Headers.groovy

  • Header ;-)

NfcoreSchema.groovy

  • Validation

@apeltzer apeltzer requested a review from a team February 16, 2021 08:49
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ewels commented Feb 18, 2021

So fast, we haven't even merged this to tools yet 😆

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apeltzer commented Feb 18, 2021

So fast, we haven't even merged this to tools yet 😆

I'm just too excited about this 🎉

jfy133
jfy133 reviewed Feb 25, 2021
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Comment thread lib/Checks.groovy Outdated
Comment thread lib/Checks.groovy Outdated
Comment thread main.nf
Comment thread nextflow_schema.json
"bt2n": {
"type": "integer",
"description": "Specify the -N parameter for bowtie2 (mismatches in seed). This will override defaults from alignmode/sensitivity.",
"default": 0,
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@jfy133 jfy133 Feb 25, 2021

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Why has this been removed (and below)?

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@apeltzer apeltzer Feb 25, 2021

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I fear that was when updating with the schema builder...?

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@apeltzer apeltzer Feb 25, 2021

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Old version of tools i suppose (1.12.X?)

@jfy133 jfy133 mentioned this pull request Feb 25, 2021
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@apeltzer apeltzer added this to the 2.3.2 Patch Release milestone Mar 10, 2021
@jfy133 jfy133 merged commit a5e32db into dev Mar 12, 2021
@apeltzer apeltzer deleted the add-fancy-help-json-for-james branch March 12, 2021 09:58
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