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migrate to nf-schema #1

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migrate to nf-schema #1

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51c3153
tweak: migrate nextflow_schema.json to nf-schema
alvaromartmart Jul 1, 2024
4bbf704
tweak: replace instances of nf-validation plugin
alvaromartmart Jul 1, 2024
0eb43f1
fix: rename definitions section
ynestin Jul 9, 2024
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -28,7 +28,7 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { validateParameters; paramsHelp } from 'plugin/nf-validation'
include { validateParameters; paramsHelp } from 'plugin/nf-schema'

// Print help message if needed
if (params.help) {
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -185,7 +185,7 @@ singularity.registry = 'quay.io'

// Nextflow plugins
plugins {
id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-schema' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

// Load igenomes.config if required
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14 changes: 7 additions & 7 deletions nextflow_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/test/master/nextflow_schema.json",
"title": "nf-core/test pipeline parameters",
"description": "testing",
"type": "object",
"definitions": {
"$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

Screenshot 2024-07-10 at 09 18 37

"input_output_options": {
"title": "Input/output options",
"type": "object",
Expand Down Expand Up @@ -300,19 +300,19 @@
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
"$ref": "#/defs/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
"$ref": "#/defs/reference_genome_options"
},
{
"$ref": "#/definitions/institutional_config_options"
"$ref": "#/defs/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
"$ref": "#/defs/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
"$ref": "#/defs/generic_options"
}
]
}
6 changes: 3 additions & 3 deletions workflows/test.nf
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Expand Up @@ -4,7 +4,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-schema'

def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
Expand Down Expand Up @@ -70,8 +70,8 @@ workflow TEST {
file(params.input)
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
// 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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The new link is https://nextflow-io.github.io/nf-schema/latest/samplesheets/samplesheetToList/

// ! There is currently no tooling to help you write a sample sheet schema

//
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