migrate to nf-schema #1
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using automatic migration from migration guide
alvaromartmart
commented
Jul 1, 2024
| // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") | ||
| // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ | ||
| // TODO: OPTIONAL, you can use nf-schema plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") | ||
| // See the documentation https://nextflow-io.github.io/nf-schema/samplesheets/fromSamplesheet/ |
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@ewels this link is no longer valid, not sure if this is something to be consider either in templates potentially including this comment, or in the automatic migration command suggested by https://nextflow-io.github.io/nf-schema/latest/migration_guide/#updating-the-name-and-version-of-the-plugin, or whether an equivalent samplesheet should be served from the updated location
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alvaromartmart
commented
Jul 10, 2024
| @@ -4,7 +4,7 @@ | |||
| "title": "nf-core/test pipeline parameters", | |||
| "description": "testing", | |||
| "type": "object", | |||
| "defs": { | |||
| "$defs": { | |||
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if $defs is correct, something's wrong with the migration guide cc @ewels
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yup: the replacement in the automatic migration script uses $defs, not defs
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Quick run of https://nextflow-io.github.io/nf-schema/latest/migration_guide to migrate this example schema.