Important! Template update for nf-core/tools v3.0.2 #545
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A full test was run locally and it passed. |
jfy133
reviewed
Oct 22, 2024
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It would be good to make a few broken samplesheets and upload to the test-data repo so we can double check the schema is working like I did here: nf-core/test-datasets#1350
Did you also check that all our meta condition checks like meta.<xxx> == null or !meta.<xxx> for optional meta fields are OK, and tags look OK, no random [] empty strings, given https://nfcore.slack.com/archives/C056RQB10LU/p1729069030926369?
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.nf-core.yml
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| repository_type: pipeline | ||
| nf_core_version: "2.14.1" | ||
| template: | ||
| author: James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler |
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You definitely need to add yourself here @LilyAnderssonLee ! and I think also needs to go in the nextflow.config and license!
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I also added myself in the README.
| @@ -28,7 +27,6 @@ | |||
| }, | |||
| "db_name": { | |||
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I wonder if this should also be made unique per tool too
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I think "uniqueEntries": ["tool", "db_name"] is sufficient. Different databases can be used with the same tool. This could be useful for certain purposes, for instance database validations.
assets/schema_input.json
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| @@ -8,13 +8,12 @@ | |||
| "type": "object", | |||
| "properties": { | |||
| "sample": { | |||
| "type": "string", | |||
| "type": ["string", "integer"], | |||
| "errorMessage": "Sample name must be provided and cannot contain spaces", | |||
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We don't have a regex corresponding to this errorMessage, should e added
| "errorMessage": "Sample name must be provided and cannot contain spaces", | ||
| "meta": ["id"] | ||
| }, | ||
| "run_accession": { | ||
| "type": "string", | ||
| "unique": ["sample"], | ||
| "type": ["string", "integer"], | ||
| "errorMessage": "Run accession must be provided and cannot contain spaces." |
| // Limit resources so that this can run on GitHub Actions | ||
| resourceLimits = [ | ||
| cpus: 2, | ||
| memory: '6.GB', |
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Should be synced with teh test.config values, e.g. memory should be 15.GB etc
And applies across all configs
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I will update the memory limit in all test configs to 15. GB.
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
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Version
3.0.2of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-3.0.2branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.
For more information about this release of nf-core/tools, please see the
v3.0.2release page.