Important! Template update for nf-core/tools v2.9 #61
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mirpedrol
approved these changes
Jul 13, 2023
nextflow_schema.json
Outdated
| @@ -206,12 +207,14 @@ | |||
| "type": "boolean", | |||
| "description": "Display help text.", | |||
| "fa_icon": "fas fa-question-circle", | |||
| "default": false, | |||
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You can remove all "default": false, this is taken into account by default and will be removed if you use nf-core schema build
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It didn't automatically remove the defaults, but I removed them manually now.
| def summary_params = paramsSummaryMap(workflow) | ||
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| // Print parameter summary log to screen | ||
| log.info logo + paramsSummaryLog(workflow) + citation |
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[This is a comment for line 29] The schema is now validating that params.input exists, so you could skip this check here.
The same stands for other file parameters, you can add the flag "exists": true in nextflow_schema.json and remove those checks from the main pipeline code :)
WackerO
reviewed
Jul 13, 2023
| @@ -189,7 +190,7 @@ | |||
| "description": "Maximum amount of time that can be requested for any single job.", | |||
| "default": "240.h", | |||
| "fa_icon": "far fa-clock", | |||
| "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", | |||
| "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", | |||
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Just to clarify: This was introduced by the update, not by you?
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yes, this is from the template update: see here
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You could also consider removing the TODOs that the update introduced :) |
Co-authored-by: Júlia Mir Pedrol <[email protected]>
Co-authored-by: Júlia Mir Pedrol <[email protected]>
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Version
2.9of 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-2.9branch (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/developers/sync.
For more information about this release of nf-core/tools, please see the
v2.9release page.