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‎src/main/groovy/nfcore/plugin/NfUtilsExtension.groovy‎

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Original file line numberDiff line numberDiff line change
@@ -23,7 +23,6 @@ import nfcore.plugin.nfcore.NfcoreConfigValidator
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import nfcore.plugin.nfcore.NfcoreVersionUtils
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import nfcore.plugin.nfcore.NfcoreCitationUtils
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import nfcore.plugin.nfcore.NfcoreReportingOrchestrator
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import nfcore.plugin.ReferencesUtils
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/**
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* Implements a custom function which can be imported by
@@ -48,20 +47,6 @@ class NfUtilsExtension extends PluginExtensionPoint {
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println "Hello, ${target}!"
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}
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/**
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* Get a genome attribute from params.genomes for the selected genome.
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* Delegates to ReferencesUtils.getGenomeAttribute().
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*
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* @param attribute The attribute name to retrieve (e.g. 'fasta', 'gtf')
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* @return The attribute value or null
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*/
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@Function
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Object getGenomeAttribute(String attribute) {
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Map params = session?.getConfig()?.get('params') as Map
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if (!params) params = session?.params as Map
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return ReferencesUtils.getGenomeAttribute(params, attribute)
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}
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// --- Methods from NfcoreExtension ---
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/**
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* Generate methods description text for MultiQC report
@@ -275,50 +260,6 @@ class NfUtilsExtension extends PluginExtensionPoint {
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return NfcoreVersionUtils.workflowVersionToChannel(this.session)
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}
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/**
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* Combine versions from mixed sources into a single YAML string
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* Works with both channels and lists
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* When given a channel, returns a channel that emits the combined YAML
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* When given a list, returns the YAML string directly
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*
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* Supports multiple calling patterns:
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* 1. Named parameters: softwareVersionsToYAML(softwareVersions: channel, nextflowVersion: workflow.nextflow.version)
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* 2. Positional: softwareVersionsToYAML(channel)
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* 3. Mixed: softwareVersionsToYAML(channel, nextflowVersion: workflow.nextflow.version)
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*
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* @param versionsOrOptions Either a channel/list of versions, or a Map with 'softwareVersions' and optional 'nextflowVersion' keys
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* @param options Optional map with 'nextflowVersion' key
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* @return Channel emitting combined YAML string, or String directly if input is a list
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*/
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@Function
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Object softwareVersionsToYAML(Object versionsOrOptions, Map options = [:]) {
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// Extract versions channel/list and nextflowVersion
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Object versions = null
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def nextflowVersion = options?.nextflowVersion
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// Handle named parameters: softwareVersionsToYAML(softwareVersions: ch, nextflowVersion: v)
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if (versionsOrOptions instanceof Map && versionsOrOptions.containsKey('softwareVersions')) {
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versions = versionsOrOptions.softwareVersions
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nextflowVersion = versionsOrOptions.nextflowVersion ?: nextflowVersion
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}
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// Handle positional: softwareVersionsToYAML(ch) or softwareVersionsToYAML(ch, nextflowVersion: v)
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else {
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versions = versionsOrOptions
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}
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// If it's a channel, return a mapped channel
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if (versions?.getClass()?.getName()?.contains('DataflowBroadcast') ||
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versions?.getClass()?.getName()?.contains('DataflowStream') ||
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versions?.getClass()?.getName()?.contains('DataflowVariable')) {
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return versions.toList().map { versionsList ->
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// Call with positional arguments in the correct order
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NfcoreVersionUtils.softwareVersionsToYAML(versionsList as List, this.session as Session, nextflowVersion)
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}
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}
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// If it's a list, process directly
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return NfcoreVersionUtils.softwareVersionsToYAML(versions as List, this.session as Session, nextflowVersion)
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}
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// --- Citation Management Functions ---
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/**
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* Generate citation for a tool from meta.yml at the module level

‎src/main/groovy/nfcore/plugin/references/ReferencesUtils.groovy‎

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Original file line numberDiff line numberDiff line change
@@ -32,54 +32,6 @@ class ReferencesUtils {
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this.session = session
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}
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/**
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* Instance convenience method that reads params from the initialized Session
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* and delegates to the static getGenomeAttribute(Map, String) implementation.
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*
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* Usage (when ReferencesUtils has been initialized with a Session):
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* def utils = new ReferencesUtils()
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* utils.init(session)
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* utils.getGenomeAttribute('fasta')
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*/
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Object getGenomeAttribute(String attribute) {
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Map params = session?.getConfig()?.get('params') as Map
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// Fallback: some Nextflow Session implementations expose params directly
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if (!params) params = session?.params as Map
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if (params) return ReferencesUtils.getGenomeAttribute(params, attribute)
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return null
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}
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/**
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* Return the named attribute for the selected genome in params, or null.
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* Returns a single value (not wrapped in a List).
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*
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* Example:
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* def fasta = ReferencesUtils.getGenomeAttribute(params, 'fasta')
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*/
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static Object getGenomeAttribute(Map params, String attribute) {
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if (params == null) return null
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final Object genomesObj = params.get('genomes')
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final Object genomeKeyObj = params.get('genome')
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if (!(genomesObj instanceof Map) || !(genomeKeyObj instanceof String)) {
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return null
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}
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final Map genomes = (Map) genomesObj
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final String genomeKey = (String) genomeKeyObj
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if (!genomes.containsKey(genomeKey)) return null
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final Object genomeObj = genomes.get(genomeKey)
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if (!(genomeObj instanceof Map)) return null
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final Map genome = (Map) genomeObj
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if (!genome.containsKey(attribute)) return null
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return genome.get(attribute)
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}
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/**
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* Get references file from a references list or parameters
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*

‎src/test/groovy/nfcore/plugin/references/ReferencesUtilsTest.groovy‎

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Original file line numberDiff line numberDiff line change
@@ -55,135 +55,4 @@ class ReferencesUtilsTest extends Specification {
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result_file == [null]
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result_value == [null]
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}
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def "test getGenomeAttribute with valid params"() {
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given:
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def params = [
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genome: 'GRCh38',
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genomes: [
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GRCh38: [
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fasta: 's3://bucket/genome.fa',
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gtf: 's3://bucket/genes.gtf',
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star: 's3://bucket/star_index/'
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],
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GRCh37: [
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fasta: 's3://bucket/genome37.fa'
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]
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]
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]
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when:
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def fasta = ReferencesUtils.getGenomeAttribute(params, 'fasta')
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def gtf = ReferencesUtils.getGenomeAttribute(params, 'gtf')
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def star = ReferencesUtils.getGenomeAttribute(params, 'star')
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then:
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fasta == 's3://bucket/genome.fa'
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gtf == 's3://bucket/genes.gtf'
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star == 's3://bucket/star_index/'
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}
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def "test getGenomeAttribute with missing attribute"() {
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given:
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def params = [
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genome: 'GRCh38',
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genomes: [
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GRCh38: [
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fasta: 's3://bucket/genome.fa'
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]
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]
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]
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when:
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def result = ReferencesUtils.getGenomeAttribute(params, 'gtf')
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then:
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result == null
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}
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def "test getGenomeAttribute with missing genome"() {
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given:
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def params = [
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genome: 'GRCh99',
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genomes: [
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GRCh38: [
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fasta: 's3://bucket/genome.fa'
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]
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]
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]
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when:
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def result = ReferencesUtils.getGenomeAttribute(params, 'fasta')
117-
118-
then:
119-
result == null
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}
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def "test getGenomeAttribute with null params"() {
123-
when:
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def result = ReferencesUtils.getGenomeAttribute(null, 'fasta')
125-
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then:
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result == null
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}
129-
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def "test getGenomeAttribute with missing genomes map"() {
131-
given:
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def params = [
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genome: 'GRCh38'
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]
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when:
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def result = ReferencesUtils.getGenomeAttribute(params, 'fasta')
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then:
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result == null
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}
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def "test getGenomeAttribute with missing genome key"() {
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given:
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def params = [
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genomes: [
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GRCh38: [
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fasta: 's3://bucket/genome.fa'
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]
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]
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]
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when:
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def result = ReferencesUtils.getGenomeAttribute(params, 'fasta')
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then:
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result == null
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}
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def "test getGenomeAttribute with different value types"() {
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given:
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def params = [
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genome: 'test',
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genomes: [
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test: [
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string_value: 'some_string',
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list_value: ['item1', 'item2'],
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map_value: [key: 'value'],
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number_value: 42,
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boolean_value: true
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]
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]
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]
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when:
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def string_result = ReferencesUtils.getGenomeAttribute(params, 'string_value')
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def list_result = ReferencesUtils.getGenomeAttribute(params, 'list_value')
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def map_result = ReferencesUtils.getGenomeAttribute(params, 'map_value')
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def number_result = ReferencesUtils.getGenomeAttribute(params, 'number_value')
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def boolean_result = ReferencesUtils.getGenomeAttribute(params, 'boolean_value')
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then:
183-
string_result == 'some_string'
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list_result == ['item1', 'item2']
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map_result == [key: 'value']
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number_result == 42
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boolean_result == true
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}
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}

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